An artificial ecosystem will eventually evolve into a social, economic and natural rural complex ecosystems. In this process, the connection between different components of its structure is a key issue for sustainable development of the ecosystem. This issue consists of three aspects: the simplieation of the structural elements, the uncompletement of the structural chain and the irrationality of the structural web. These stems mainly from the unharmony between structural diversity and dominance, structural openness and independence during the process of systems management. That is to say the relationship between stability and the speed of the systems is not balanced. A good planning and design will be favorable for promoting the sustainability of the systems. Little attention has been paid to the research on the relationship between the structure and sustainability of rural complex ecosystems of different structural types. Based on a series of case studies, for example, farmland ecosystem, agricultural ecosystem and rural ecosystems, this paper focuses mainly on the dynamic mechanisms, cybernatic principles, and the engineering approaches concerning the relationship between the sustainable development and the structural characters of the rural complex ecosystems. Main results are as follow: The evoluation of natural ecosystem from farmland ecosystem to rural complex ecosystem reflects the dynamic of structure from simple to complex, single to diversity. It is also an important way to utilize agricultural resource comprehensively, to enrich products, to industrialize and proportionize production. The dynamic mechanisms of rural complex ecosystem consist of resources niches, consumption requirements, scientific technologies, policies and cultures. Competition, coexisting, recycling and self-resiliency are the four cybernetics principles of the system. Four factors infleunce the sustainable development of the system, namely, structural diversity, dominance, openness and independence. The structure of rural complex ecosystems covers structural elements, chain and web. The structural elements are composed of environments, organisms, industries and management. The structural chains are composed of production, processing, consumption, resource utilization, pollutants treatment chains etc., The structural webs are composed of resource and environment, producting, market, infrastructure, culture and information webs. The diversity of structure refers the diversity of structural elements, chains and webs at different levels. The diversity of elements means the diversity of living organisms, industries, physical environments and management components. Diversity of chains reflects the degree of chain combination of materials, energy and information driven by some single aim and function, such as resource exploitation, production, environmental management and the progress of society. Diversity of webs reflects the degree of intercombination between different chains at systemetic level. It is very easy for man to recognize the diversity of elements, while the diversities of structure and function in chains and webs are always reglected. The function of system is evaluated with three indexes. Dominant component, chain and web are three parts of structural dominance which are settled by structural sensitivity. The openness is formed by resources, market, energy, intelligence, information and policy. The relation between diversity and stability of a structure is a non-linar web which is related with dominance, openness and independence, rather than a linar relation. The harmony between diversity and dominance, openness and independence dominantes the relation between diversity and stability. Structural diversity and independence are the decisive factors stablizing the development of ecosystem while dominance and openness are the decisive factors of the ecosystem growth. Harmony between the stability and the increase of an ecosystem is the unique factor leading system develop sustainably. Systemetic study on 18 types of farmland ecosystems with different amount of organisms such as one, two, three and more than three organisms shows that the properly increase of the varieties and the amount of biomass actors can be favorable for the boosting of economic productivity and the enhancement of the stability of system. Its prerequistite is certain amount of input of cash, technology, materials, information and certain degree of elements' heterogeneity. Analysis to four kinds of farmland ecosystems, that is, monoculture, intercropping between wheat and corn, corn and soybean, and rice, duck and fish, shows that the structural diversity indexes of each are 0, 0.095, 0.187, and 0.446, respectively; while the dominance indexes are 1, 0.910, 0.842 and 0.478, respectively. Meanwhile, the average economic productivity of three-component system is 1.78 and 2.77 times more than the couple and single component ecosystems. Results also reveal that the rates of light energy utilization in several, couple and single components systems are 1.17, 0.68 and 0.35, respectively. A tendency of the improvement of soil chemical properties and the decrease of deseases, insects and weed in the systems is found following with the increase of organism components. So, we can conclude that one farmland ecosystem with rational combination of several components has the highest stability and function, and single element ecosystem is a most unsustainable farmland ecosystem. Strong evidence can be abserved from a farmland ecosystem consisting of rice, duck and fish in which the indexes of structural diversity and dominance are 0.4460 and 0.4777, respectively. To uncover the rules of agricultural ecosystem, three kinds of cases are selected.