Rice serves as a vital staple food, but its accumulation of cadmium (Cd) has sparked widespread concerns regarding food safety and ecosystem security. Here, we conducted a seven-year systematic field experiment in the Xiangjiang River Basin of China, where an integrated governance framework (IGF) was established to ensure rice safety. The IGF, tailored to geographical zoning and pollution gradation, includes targeted soil treatments, crop management strategies, and stakeholder engagement. The quality of both the soil and the crop was improved, with a reduction in soil Cd availability of 36%, and a decrease in Cd in rice grain of 57-78%. This framework not only addresses multiple challenges but also supports sustainable development goals (SDGs 2, 3, 6, 9) by fostering comprehensive synergies among science, policy, and local community participation. Our findings provide empirical guidance for safe rice production in Cd-contaminated areas and provide solid scientific-driven decision support globally.