The invention relates to a microorganism cleaning bactericide capable of removing multiple poisonous and harmful substances and a preparation method thereof. The microorganism cleaning bactericide comprises the mixture of compound balsamic extract liquor and the fermentation product of compound microbial bacterium system protospecies liquid in an industrial fermentation culture solution. The invention utilizes the high-efficiency adsorption, assimilation and metabolism of the microbial bacterium system to purify and treat aldehydes, benzenes, alcohols, esters, phenols, amines, alkanes, sulfur-containing substances, TVOC, putrefying bacteria secreta, obnoxious gases of pathogenic bacteria, pathogenic bacteria secreta and the like, or the harmful substances of the solution thereof by the degradation and decomposition processes; harmful substances, such as formaldehyde, benzene, volatile organic compounds and the like in environment, which are released by housing decoration, office furniture and new car decoration, are converted into nontoxic, harmless and scentless substances; and meanwhile, the invention also performs the functions of sterilization to the pathogenic bacteria and the secreta thereof and realizes the targets of thoroughly improving air quality and protecting the health of people.