To fulfill sustainability principles, a three-site field experiment was conducted to screen suitably mixed passivators from lime + biochar (L + C, 9000 kgha−1 with a rate of 1:1) and lime + biochar + sepiolite (L + C + S, 9000 kg ha−1 with a rate of 1:1:1), in Yuecheng (YC), Zhuji (ZJ), and Fuyang (FY), where there are typical contaminated soils, in South China. Treated with passivators in soil, DTPA-extractable Cd, Crand Pb in soil were decreased by 9.87–26.3%, 37.2–67.5%, and 19.0–54.2%, respectively; Cd, Cr, and Pb in rice were decreased by 85.9–91.5%, 40.0–76.5%, and 16.4–45.4%, respectively; and these were followed by slightly higher efficacy of L + C + S than L + C. The differences between L + C and L + C + S mainly lie in soil microbial communities, enzymes, and fertility. In YC, treatment with L + C + S increased microbial carbon and activities of urease (EC3.5.1.5) and phosphatase (EC3.1.3.1) by 21.0%, 85.5%, and 22.3%; while treatment with L + C decreased microbial carbon and activities of phosphatase and sucrose (EC3.2.1.26) by 1.31%, 34.9%, and 43.4%, respectively. Moreover, the treatment of FY soils with L + C + S increased microbial carbon and activities of urease, phosphatase, and sucrase by 35.4%, 41.6%, 27.9%, and 7.37%; and L + C treatment only increased the microbial carbon and the activity of phosphatase by 3.14% and 30.3%, respectively. Furthermore, the organic matter and available nitrogen were also increased by 8.8–19.0% and 7.4–14.6% with L + C + S treatments, respectively. These suggested that the combination of L + C + S stimulated the growth of soil microbial communities and increased the activity of soil enzymes. Therefore, the L + C + S strategy can be a practical and effective measure for safe rice production as it was more suitable for the remediation of heavy metals in our experimental sites.