With the intensification of human activities, the amount of phosphorus (P)-containing waste has increased. When such waste is not recycled, P is released into the environment, leading to environmental issues such as the eutrophication of water bodies. In this study, based on the material flow analysis method, a P Waste Flow analysis model (P-WFA) was developed to analyze the P flow in the waste system of Poyang Lake, the largest freshwater lake in China. To address the research gap in long-term P flow analysis at the watershed scale, this study quantified the P content in the waste system of the Poyang Lake Watershed from 1950 to 2020. The analysis revealed that from 1950 to 2020, the total P input into the waste system increased from 5.49 × 104 tons in 1950 to 2.28 × 105 tons in 2020. The breeding industry system was identified as the primary source, accounting for 25.19–41.59 % of the total waste system. Over the past 70 years, P loss to surface water from waste systems has been primarily facilitated by manure from the breeding industry, as well as drainage from crop farming systems (77.74 % in 2020). At the same time, the P recycling rate (PRR) of the waste system exhibited an initial increase followed by a decrease, increasing from 44.14 % to 47.75 % before dropping to 44.41 %. Population growth, urbanization, and changes in consumption levels in Jiangxi Province have led to changes in the dietary structure and fertilizer use, consequently affecting the P cycling pattern. This study presents a comprehensive P flow model for waste systems in the Poyang Lake Watershed. This model can be used as a reference to enhance P cycling and manage P loss in other large freshwater lakes. © 2024 Elsevier B.V.