The fertilizer reduction and green manure application experiments were conducted to study the nitrogen and phosphorus loss in runoff and the rice yield under double cropping rice system. The results indicated that 20% amount of urea and 30% of phosphorus reduction could make a change of the rice yield from –11.48% to 1.94%. When the application of both sulfur coated urea and phosphorus were reduced 30% respectively, the rice yield changed from –13.24% to 3.87%. When both nitrogen and phosphorus were cut 30 percent down from compound fertilizer, the rice yield, however, increased by 0.52%–13.70%. The amounts of nitrogen loss could be reduced from 31.69% to 47.74% and that of phosphorus from 11.77% to 64.71% in runoff by the way of reducing fertilizer utilization. The utilization rate of nitrogen and phosphorus could be increased by 19.31% and 11.97% respectively when the compound fertilizer was employed in double cropping rice system. In the context of little impacts on rice yield, fertilizer reduction could improve its utilization rate, and reduced agricultural input, such as nitrogen and phosphorus.