As the main composition of photo-chemical smog and one of the most detrimental secondary pollutants, ozone (O3) has been widely notorious for its phytotoxic effects on terrestrial plants. Wide attention has recently been focused on the agricultural product loss resulted from the elevated O3 concentration near the land surface. Nevertheless, the majority of previous researches concentrated on its effects on above-ground parts of crops, like photosynthetic physiology, while less on other potential parts. Currently greenhouse effect has been the most concerned issues in climate changes; as the two primary forms of greenhouse gases, variations in the concentration of carbon dioxide (CO2) and methane (CH4) have also attracted substantial interests of researches. Agroecosystem is the principal source of these listed greenhouses gases, and there are a multitude of field experiments conducted with respect to the mechanisms and processes of the generation of CO2 and CH4. However, considering the situation of increasingly elevating O3 concentration, the trend of emission of CO2 and CH4 in agroecosystem still remains uncertain. In this study, with the improved approach of OTC combined with laboratory experiments and analysis, we studied the influences of elevated O3 concentration on soil respiration, CH4 emission as well as the allocation of nutrition element and grain quality, thereby providing a scientific basis for accurate assessment of the effects of elevated O3 concentration. Main derived results are as follows.