The invention relates to a microbial agent. The microbial agent is formed by three fungi including mortierella, trichoderma asperellum and mucor circinelloides. The fungi are activated, propagated anddiluted into 1-9*10<7>CFU/ml fungal liquid respectively, and the three types of fungal liquid are subjected to isovolumetric mixing to obtain the microbial agent. The application of the microbial agent to passivation of heavy metals in soil refers to a method of plant infection with the microbial agent to form infected okra, alfalfa and soybean plants, and removal rates of copper, zinc, lead, cadmium and manganese is 75.69%, 57.60%, 89.61%, 82.83% and 68.77% respectively. Preparation and application methods of the microbial agent are simple and economical, soil physiochemical properties can be effectively improved, fertilizer and water retention capacity of soil is increased, secondary pollution is avoided, and a short application period is realized.