The present invention relates to a microbial agent for treating heavy metal polluted soil, a preparation method and applications thereof. The microbial agent comprises the following raw materials: rice husk, pig manure, chicken manure, soybean powder, single cell protein, a Mortierella alpina fermentation broth, a Trichoderma asperellum fermentation broth, and a Mucor circinelloides fermentation broth. According to the present invention, the microbial agent prepared by mixing Mortierella alpina, Trichoderma asperellum and Mucor circinelloides according to a certain ratio is firstly used, can be used in the complex and changing environment, and can provide effects in the poor soil environment, wherein the functional microbes provide high tolerance to heavy metals, and can maintain activity and perform efficient repair in the heavily heavy metal polluted soil.