The present invention discloses a composite microbial deodorant and a preparation method thereof. The composite microbial deodorant contains Rhodop seudanonas palustris, Candida utilis, Lactobacillus acidophilus, Streptomyces griseus and Bacillus subtilis, wherein the Rhodop seudanonas palustris, the Candida utilis, and the Lactobacillus acidophilus are subjected to mixed fermentation in a light-transmitting temperature-controllable fermentation tank, the Streptomyces griseus and the Bacillus subtilis are subjected to mixed fermentation in an aerating sterile air temperature-controlled fermentation tank, and the two fermented bacterial agents are mixed and added with essence, citric acid and glacial acetic acid to prepare the composite microbial deodorant. The composite microbial deodorant of the present invention has characteristics of simple preparation process and no secondary pollution, and provides good odor removing effects for toilets, farms and other occasions.