Pesticides applied worldwide to meet food demand is recognized as a key threat to the Sustainable Development Goals (SDGs) set by the United Nations. Studies on pesticide risks employ different ingredients, methods or specific environments, which makes it difficult to quantify the scale of the problem. Furthermore, the complex influences and hotspots of long-term pesticide usage remain unclear. Herein, we present a national-scale study of four typical pesticides in China, the world’s largest pesticide user. The spatiotemporal changes in legacy and risk of pesticides over 30 years were analyzed using a modified fugacity model approach coupled with comprehensive ingredient database. Pesticide risk in mainland China might last until 2075 due to the previous legacy, although the usage has declined since 2014. The use of target pesticides was estimated as 2.38 × 105 tonnes in 2017, and about 6.59 × 103 tonnes discharged into the ocean from major basins. Risk areas expanded from 47% in 1991 to 79% in 2017, with 30% at high risk. Of the risk areas, 31% were highly populated while 3% had high biodiversity. 7% of mainland China suffered from both limited water resource and high pesticide risk. It is shown that the improper substitution with lower toxicity pesticides would make the proportion of high-risk regions unexpectedly increased from 18% to 44% due to the longer half-lives of the alternatives. Pesticides pose risks to environmental and human health, and the tailored assessment tool will be vital in contributing towards future pesticide management and meeting sustainability targets in China.