Phosphorus (P) is an essential nutrient for crops, playing a critical role in plant growth and development. Adequate P availability in the soil is closely tied to crop productivity and soil health. Integrated rice-duck farming has been known for its sustainable and eco-friendly practices. However, the specific effects of this farming system on soil P fractions as well as the mechanisms by which it influences P use efficiency (PUE) by crops, require further investigation. Here, we conducted a two-years field experiment of integrated rice-ducking farming combined with four fertilizer treatments, including chemical fertilizer (RDF), a mixture of 70 % chemical and 30 % organic fertilizers (RDFO), organic fertilizer (RDO) and no fertilizer (RD). The control groups with absence of ducks (rice monoculture) were also set based on the consistent fertilizer treatments as RMF (chemical fertilizer), RMFO (a mixture of 70 % chemical and 30 % organic fertilizers), RMO (organic fertilizer) and RM (no fertilizer applied), respectively. The input of P, nitrogen and potassium fertilizer were consistent among treatments. The results demonstrate that the integrated rice-duck farming system significantly enhances soil labile phosphorus pools, thereby improving P use efficiency (PUE) and ultimately increasing rice yield, particularly under chemical and mixed fertilizer regimes. The presence of ducks was found to increase the labile P fractions in the soil, such as Resin-P and NaHCO₃-P, which are directly available to plants. This further lead to a substantial increase in PUE than rice monoculture. RDF significantly increased PUE by 41.3 % and 20.5 % in 2018 and 2019, respectively. RDFO significantly increased PUE by 10.9 % and 26.1 % in 2018 and 2019, respectively. Only under organic fertilizer treatment there was no significant difference for grain P uptake or PUE between the treatments with or without the presence of ducks. Furthermore, RD significantly improved the grain yields by 15.3 % and 8.83 % in 2018 and 2019, respectively. RDFO only significantly increased the grain yields by 9.6 % in 2019. These results demonstrate a sustainable approach to improve P fertilizer management in rice cultivation, potentially leading to higher crop productivity and better PUE. Further long-term studies, especially under organic fertilizer regimes, are necessary to explore the potential environmental impacts of this integrated farming system.