Nutrient use efficiency has decreased in southwest China since 2009 with increasing risk of nutrient excess

The optimal application of nutrients, such as nitrogen and phosphorus, to the soil is crucial for achieving high crop yields with minimal environmental impact. However, the effect of spatio-temporal changes in soil nutrient supply on crop yield is poorly understood in China. Here, we present a framework that combines environmental data, fertilizer field experiments, and machine learning to estimate the rice yield responses to different nutrient conditions and overall farmland nutrient sustainability in southwest China from 2009 to 2019. The results show that the fertilizer input has contributed to the long-term increase in rice yield over the past ten years. The fertilizer use has increased rice yield by 2.3–2.4 tons per hectare per year. However, the nutrient use efficiency decreased, with the fertilizer contribution ratio declining from 29.3% in 2009 to 27.5% in 2019. Further, 19% of the rice-growing farmlands are at risk of nutrient excess, and 36% are at risk of nutrient degradation. Controlling nitrogen and phosphorus input is key to nutrient regulation, and our approach may guide the sustainable use of nutrient resources on farmlands.