Phosphorus (P) is a critical macronutrient in rice-paddy systems, essential for crop productivity. However, inefficient P management often leads to significant environmental issues such as nutrient leaching and eutrophication. This study investigated the impacts of different fertilization strategies conventional chemical fertilization (CT), partial organic substitution (MT), and fully organic fertilization (OT)—on P transport, rice yield, and environmental risks over a seven-year period. Using a combination of field experiments and HYDRUS-1D simulations, we analyzed how agricultural management influences P distribution in the soil profile, crop uptake, and leaching potential. Our results showed that HYDRUS-1D model could accurately simulate P transport, with RMSE range from 0.024 to 0.031 mg L−1 during calibration in 2012 and 0.053–0.073 mg L−1 during validation in 2018. The results demonstrated that the MT treatment achieved the highest P use efficiency, maintaining rice yields comparable to CT while significantly reducing P leaching into deeper soil layers. In contrast, OT resulted in excessive P buildup in the topsoil, increasing leaching risks. Model simulations further show that an increase in temperature by up to 2°C had minimal effects on P transport, suggesting that proper P fertilization strategies are more critical than temperature variability for minimizing environmental pollution. According to model simulation, the recommended P application rates for CT, MT, and OT are 64.18, 55.86, 50.97 kg hm−2 respectively, with MT providing the best balance between crop productivity and environmental sustainability. Overall, this study offers novel insights into how mixed fertilization practices can optimize P management in rice-paddy systems, contributing to sustainable agriculture by reducing P losses and enhancing environmental protection. Future research should assess the long-term applicability of these strategies across diverse agricultural landscapes.