Although rubber-based (Hevea brasiliensis) agroforestry systems are regarded as the best approach to improving the sustainability of rubber agriculture and environmental conservation, soil physico-chemical properties and their related interactions have rarely been examined in such systems. The objective of this study was to examine the management and landscape effects on soil structure, soil moisture and soil nutrients in the Xishuangbanna region. The treatments were tropical rain forest (TRF), rubber monoculture (Rm), and two rubber-based agroforestry systems: H. brasiliensis-T. cacao (HTAs) and H. brasiliensis-F. macrophylla (HFAs). The results showed that after approximately three decades of the conversion from tropical rain forest to rubber monoculture, soils in the rubber plantations suffered serious degradation (poor soil physical properties, poor soil structure, limited soil moisture, unstable aggregates, depleted nutrients and serious soil erosion). However, the rubber-based agroforestry systems (both HTAs and HFAs) evidently improved the soil physical properties and enriched the soil nutrients in the rubber plantations. Compared to the corresponding values in rubber monoculture, the total soil porosity, initial soil moisture, soil mean weight diameter (MWD) and soil hydraulic conductivity (K,) in rubber-based agroforestry systems increased, on average, by 13.3%, 54.7%, 31.5%, and 246.4%, respectively. In addition, the nutrients of C, N, P, Ca and Mg increased, on average, by 38.8%, 38.5%, 48.2%, 47.9% and 31.4%, respectively, after the transformation from rubber monoculture to agroforestry systems. Our results clearly indicated that the soil physico-chemical properties of rubber plantations were improved by interplanting, and the patterns of the intercropping system could play key roles in promoting the sustainable development of agriculture and the environment.