Abstract: In recent years, excessive input and inefficient utilization of nitrogen and phosphorus in the cropping system of the Poyang Lake Basin have led to significant losses of these elements, resulting in persistent exceedances of nitrogen and phosphorus standards, as well as other environmental issues. Therefore, quantitatively tracing the spatiotemporal patterns of nitrogen and phosphorus metabolism in the cropping system of Poyang Lake Basin is crucial for ensuring the sustainability of the basin"s ecosystem. This study applied the Material Flow Analysis (MFA) method to investigate the spatiotemporal variations of nitrogen and phosphorus fluxes in cropping systems across the Poyang Lake Basin from 2000 to 2022.Four scenarios were designed based on the current status of nitrogen and phosphorus pollutant emissions: a baseline scenario, a scenario with reduced fertilizer inputs to arable land, a scenario with increased straw recycling rates, and a scenario with comprehensive measures. The emission reduction potentials was quantitatively calculated under various scenarios and finally the optimal strategies for nitrogen and phosphorus pollutant emission reduction and prevention were proposed. The results show that the nitrogen and phosphorus inputs in the basin initially increased, then fluctuated stably, peaking around 2015. Spatially, the total nitrogen and phosphorus inputs are highest in the coastal lake district, reaching 281,000 tons of nitrogen and 64,000 tons of phosphorus, respectively, with chemical and organic fertilizers accounting for over half of the total inputs. In terms of the nutrient use efficiency, the combined use rate of nitrogen and phosphorus were 48.5% and 31.0% respectively. The nitrogen and phosphorus utilization rates for all crops has declined since 2010, and the nutrient input nitrogen and phosphorus ratio has also decreased continuously, with an average N/P of 3.9. Scenario analysis suggests that implementing measures to reduce chemical fertilizer use could decrease nitrogen output by 150,000 tonnes by 2050, nitrogen and phosphorus emissions can be reduced by 159,000 tons, reducing pollutants by 53.4%. compared with the baseline scenario, the ratio of N/P discharged into the environment can rise to 6.5. Reducing fertilizer application accounts for 75.7% of the emission reduction, demonstrating its effectiveness as a mitigation strategy. By quantitatively analyzing the nitrogen and phosphorus structure of cropping system and tracing the nitrogen and phosphorus inputs over the past 20 years in Poyang Lake Basin, identifying and judging the change trend of the nitrogen and phosphorus ratio, This analysis allows us to systematically evaluate the key processes of the agricultural system and provides a scientific basis for developing effective integrated nitrogen and phosphorus management measures in the Poyang Lake Basin by evaluating the potential outcomes of future scenarios.