In order to explore the optimum fertilization model for reducing the loss of phosphorus in farmland and improve the utilization ratio of phosphate fertilizer in the Yangtze River Basin, as well as reduce the threat to the water quality of the Yangtze River, a long-term field experiment and laboratory analysis were carried out to study the effect of phosphate fertilizer and phosphorus element transportation on chemical fertilizer application combined with pig manure and rice straw in purple soil. The results showed that the application of reduced chemical fertilizers combined with organic fertilizer did not significantly affect crop yield, and to some extent it could reduce agricultural phosphorus loss and improve phosphorus utilization. The utilization rate of phosphate fertilizer by rice showed that pig manure+20% reduced conventional phosphorus fertilizer (MDP)＞straw+20% reduced conventional phosphorus fertilizer (SDP)＞pig manure+conventional phosphorus fertilizer (MP)＞straw+conventional phosphorus fertilizer (SP)≈optimal fertilizer (P), with the utilization rate of phosphate fertilizer between 20% to 25% in all treatments. The utilization rate of phosphate fertilizer of rape listed in the order of SDP＞MDP＞MP＞SP＞P, with the utilization rate of phosphate fertilizer between 17% to 29%. In the first month of rice growth period, total phosphorus content in field surface water increased with the increase of the levels of phosphorus fertilizer, and that in the conventional fertilization (P) treatment was 4 times higher than that in no P fertilizer (P0). The phosphorus content listed in the order of P＞MP＞SP＞MDP＞SDP＞P0. Combined application of organic manure in paddy soil could improve the phosphorus fixation and reduce early phosphorus release to the water, and straw showed better effect than pig manure. The critical period of field control of phosphorus loss was 7 to 10 days after adding P fertilizer into the field. The available P content was much lower in bud stage of rape than in seedling stage, but it increase significantly in flowering stage and the later stage of rape. It was the main period of soil phosphorus leaching after flowering period of rape. The application of organic and inorganic fertilizer could significantly increase the content of available phosphorus in soil, and chemical phosphate fertilizer reduction and combined application of organic fertilizer is a good measure to deal with “control source and curb loss” of agricultural non-point source pollution.