The invention discloses a novel safety efficient biological deodorant and a preparation method thereof. The novel safety efficient biological deodorant comprises beneficial bacteria agents, plant extracts and biological enzyme, wherein the beneficial bacteria agents comprise lactic acid bacteria, bacillus subtilis, bacillus megatherium, filamentous fungi, actinomycetes, saccharomycetes and photosynthetic bacteria, the plant extracts comprise green tea extracts, grape seed extracts, yucca extracts and celery seed extracts, and the biological enzyme comprises aspartic protease and papain. The preparation method includes the steps: culturing the lactic acid bacteria, the bacillus subtilis, the bacillus megatherium, the filamentous fungi, the actinomycetes, the saccharomycetes and the photosynthetic bacteria to a plateau and then mixing and adding the lactic acid bacteria, the bacillus subtilis, the bacillus megatherium, the filamentous fungi, the actinomycetes, the saccharomycetes and thephotosynthetic bacteria into a culture medium to obtain a total culture medium; adding the beneficial bacteria agents into the total culture medium and uniformly mixing the beneficial bacteria agents; finally, adding the plant extracts and the biological enzyme into the total culture medium, uniformly mixing and stirring the plant extracts and the biological enzyme and preserving mixture to obtain the biological deodorant.