Zizania-rice rotation system was established and treated by 3 fertilizing methods. We analyzed the effects of fertilizer treatments on the environment and crop yield of zizania-rice rotation system. Results showed that the organic fertilizer was beneficial to zizania-rice rotation system both in ecological terms and for soil fertility. Soil in that cropping system had the lowest bulk density (1.15 g/cm³) and highest total porosity (54.92%), while the water storage capacity was 27.36 mm. The system also had the highest zizania yield (74,800 kg/ha). There was no significant difference on rice yield among the cropping system treated by different fertilizing methods.