Little is known about the effect of the long-term application of organic and inorganic fertilizers on P-use efficiency, P budget, and the residual effect of P fertilizer. To clarify the effect of different fertilization on soil P balance in a rice (Oryza sativa L.)–wheat (Triticum aestivum L.) rotation system is helpful to promote the sustainable development of agriculture. Thus, a thirty-five-year fertilizer experiment was conducted with eight treatments, including an unfertilized control (CK); chemical nitrogen (N), phosphorus (P), and potassium (K) fertilizers; and organic manure (M) either alone or in combination treatments (N, NP, NPK, M, MN, MNP, and MNPK). The results indicated that crop yields and P uptake were higher in the combined application of manure and chemical fertilizer treatments than in the manure or chemical fertilizer alone treatments. Soil P budget indicated a 23.4–55.4 kg P ha−1 yr−1 surplus in the organic combined with or without mineral fertilizer treatments, but the soil P budget indicated a 20.0 and 21.9 kg P ha−1 yr−1 deficit in the control and N treatments. The proportion of residual fertilizer P converted to soil available P in NP, NPK, M, MN, MNP, and MNPK treatments was 4.5%, 4.8%, 19.1%, 19.0%, 11.5%, and 13.3%, respectively, over a 35-year period. Furthermore, according to the higher P content and crop uptake in organic manure treatment compared with chemical P fertilizer alone, an organic addition could effectively reduce the use of chemical fertilizer and become an effective way of sustainable development in practice. Therefore, the combined application of organic and inorganic fertilizer will be a practical method to increase crop yields and soil P status in a rice–wheat planting system.
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