The invention discloses a microbial deodorant as well as a preparation method and application thereof. The microbial deodorant comprises bacillus and filamentous fungus. The preparation method comprises the steps of: uniformly mixing bacillus fermentation liquor and filamentous fungus fermentation liquor, and preparing the mixed liquor into lyophilized powder according to the conventional method in the field; or only uniformly mixing microbial fermentation liquor and excipient liquor; or only uniformly mixing the bacillus fermentation liquor and the filamentous fungus fermentation liquor. The microbial deodorant is simple to prepare and can be used for quickly removing peculiar smells and simultaneously removing smelly-source substances completely.