Different heavy metals have different soil chemical properties. Simultaneous inactivation of the Compound heavy metal in the soil has become a bottleneck problem to be solved in soil pollution remediation. By using the natural Cd, Pb, Cu, As compound polluted soil as the research material and by setting CK (blank) and limestone (conditioner control) as two controls, a soil pot experiment was employed to understand the effects of three silicon-based conditioners (potassium silicate, manganese-potassium silicate (manganese chloride 10%+potassium silicate 90%), sulfur-potassium silicate (sodium hydrosulfide 2.5% + potassium silicate 97.5%)) on the transformation of heavy metals in soil, the accumulation of Cd, Pb, Cu, As and nutrient elements in rice , and the rice growth and antioxidant stress response. The results showed that all the three silicon-based conditioners had significantly higher capability on reducing Cd than the conditioner control (limestone). Compared with CK, the three Si-containing passivators reduced the content of Cd and Pb in brown rice by 30.0%, 45.5%, 35.6% and 56.6%, 62.6%, 37.1%, respectively, and manganese-potassium silicate had the best effect, and however, all the passivators had no significant role in reducing Cu and As in rice. Each conditioner could promote rice nutrient absorption and antioxidant capability, increased soil pH, and decreased the proportion of exchangeable Cd and Pb in soil. In conclusion, the application of silicate and its Mn and S modified mixing significantly reduces the content of Cd and Pb in brown rice, and could be used in remediation of rice Cd/Pb compound pollution.