The invention provides a phytochelatin microbial agent and a preparation method thereof. The microbial agent comprises plant active peptides, bacillus natto bacterial liquid, pichia pastoris bacterial liquid, lactobacillus casei bacterial liquid, erycibe obtusifolia benth extract, ulva powder, gallnut powder, ferrous sulfate, potassium fulvic acid and a chelating agent component. In the bacillus natto bacterial liquid, the content of bacillus natto is 40*10<9>CPU/ml; in the pichia pastoris bacterial liquid, the content of pichia pastoris is 16*10<9>CPU/ml; in the lactobacillus casei bacterial liquid, the content of lactobacillus casei is 22*10<9>CPU/ml; in the chelating agent is a mixture consisting of EDTA and calcium superphosphate at a weight ratio of 3.5:1. The content of functional bacterium in the microbial agent is (4.8 to 5.2)*10<9>/g, the content of trace elements is 42 to 45 mg/g, and the infectious microbe rate is 4.5 to 5.2 percent.