In order to explore the spatial distribution of organic phosphorus in the sediments of the rivers entering Lake Hongze and the effects of exogenous inputs on its fraction transformation, we used the Ivanoff method to study the fraction characteristics of organic phosphorus in these sediments. The long-term effects of exogenous substances on the fraction changes of organic phosphorus in sediments were also investigated by adding organic matter and iron ions in the laboratory. The results showed that the contents of organic phosphorus in the sediments of the rivers entering Lake Hongze ranged from 34.8 mg/kg to 398.6 mg/kg, accounting for 7.7% to 36.9% of the total phosphorus, and which showed non-active organic phosphorus (NOP) > middle-active organic phosphorus (MLOP) > active organic phosphorus (LOP). The average proportion of LOP in the sediments of Suihe River was 19.4%, which was higher than that of other rivers. The average proportion of NOP in Chengzi River was 56.41%, which indicated that the spatial distribution of organic phosphorus was uneven. Overall, the contents of total nitrogen, total phosphorus and organic phosphorus in sediments of Anhe and Suihe rivers were significantly higher than those of Chengzi and Huaihe rivers, indicating that the former two rivers had a higher pollution level. Redundancy analysis showed that the fractions of organic phosphorus in river sediments were affected by their physicochemical properties, indicating the different influencing factors for different pollution levels of sediment. The addition of exogenous substances can mineralize organic phosphorus in sediments and promote their transformation from NOP to LOP and MLOP. The change range of organic phosphorus fraction caused by organic matter was greater than that caused by iron, and the transformation effect of exogenous substances on organic phosphorus in heavily polluted sediments was more significant. Therefore, it is an effective way to reduce the bioavailable phosphorus of Lake Hongze by reducing the discharge of exogenous pollutants around rivers.