Phosphorus (P) loss from farmland is one of the important sources of agricultural non-point source pollution, and colloidal P (P_coll) is an important form due to its large specific surface area, strong adsorption and migration capacity. In order to evaluate the activity and loss potential of P_coll in paddy soil under different organic substitution methods, this study relied on a long-term experiment of rice-wheat rotation under two partial substitution methods of organic fertilizers (N and P fertilizer application control and N fertilizer application control only) to explore the changes in soil P_coll content and its loss risk, as well as its relationship with different P components and soil chemical properties. The treatments of N and P fertilizer application control (4 a) included no P fertilizer (CK), chemical fertilizer (CF), and pig manure instead of 30% chemical P fertilizer (OF); the treatments of control N fertilizer application only (24 a) included no fertilizer (CK), chemical fertilizer (CF), and pig manure instead of 40% chemical N fertilizer (OF). The results showed that, for the fertilization of N and P control, there were no significant differences in soil organic carbon (SOC), P_coll content and colloidal phosphorus loss potential (LPP) between the organic substitution treatment and the chemical fertilizer treatment. The proportion of soil MRP_coll (R_MRP, MRP_coll/TP_coll) was significantly (P<0.05) reduced by 1.76% than that of the chemical fertilizer treatment. For the fertilization of N control only, soil P_coll and SOC content of organic substitution treatment were 13.08 mg/kg and 20.19 g/kg, respectively, which were significantly (P<0.05) increased by 78% and 212.6% compared with the application of chemical fertilizer alone; soil LPP and R_MRP were significantly (P<0.05) increased by 1.89% and 16.05%, respectively. Soil P_coll was positively (P<0.01) correlated with soil TP, TSP, Olsen-P and CaCl₂-P under the two organic substitution methods. Soil P_coll had no significant correlation with SOC under the fertilization of N and P control, however showed a significant positive correlation (P<0.01) under the fertilization of N control only. Compared with the treatments of N and P fertilizer application control, the long-term application of organic fertilizer with only N control significantly increased the content of SOC, P_coll and different active P components in the soil, thus may induce the risk of phosphorus loss. Therefore, equaling nutrient application is a feasible organic substitution fertilization to reduce the P loss in farmland.