The invention discloses a heavy metal composite passivating agent used for paddy soil and a preparation method thereof. The heavy metal composite passivating agent is prepared from three raw materials, namely meerschaum mineral powder, iron and manganese oxides and quicklime, in proportion by the following steps of: A, preparing the meerschaum mineral powder; B preparing the iron and manganese oxides; and C, uniformly mixing the raw materials prepared in the steps A and B with the quicklime to obtain the composite passivating agent. The heavy metal composite passivating agent has a reasonableformula, the method is easy and simple to operate; and the heavy metal composite passivating agent can reduce 70.5 to 95.0 percent of the content of the effective components of meerschaum with heavy metal activity, the iron and manganese oxides (Fe2O3+MnO2), calcium oxide (CaO) and the like in the soil, and also has multiple functions of passivating soil heavy metals, restoring acidified soil andthe like, can reduce the contents of active cadmium and lead in the soil of a polluted paddy field by 39.7 to 53.8 percent and 49.9 to 59.1 percent respectively, lower the contents of the cadmium andthe lead in agriculture products by 35.1 to 46.9 percent and 35.3 to 53.1 percent respectively, and simultaneously improve the pH value of the soil by 0.22 and 0.43. The heavy metal composite passivating agent is mainly used for paddy production of extensive heavy metal pollution zones, and can also be used for the productions of corns, vegetables and the like planted in paddy fields.