The invention discloses a composite microorganism viable bacteria preparation, which contains pediococcus, yeast and bacillus with the total bacteria count of more than 1 billion per gram. The invention also discloses a method for preparing the composite microorganism viable bacteria preparation, which comprises the following steps: performing amplification liquid culture on various strains respectively according to a conventional method in the field; mixing the materials according to a required proportion; and performing solid fermentation, drying and pulverization to obtain the composite microorganism viable bacteria preparation. The invention also discloses application of the composite microorganism viable bacteria preparation in preparing an organic waste water purifying agent and an aquaculture water body purifying agent, a deodorizer, a degreasing agent or an agent for removing pipe blockages for the hygiene of a refuse tip, a public place, an agricultural product market or a kitchen, feed additives in poultry and animal husbandry or pet culture, and preparations for controlling agricultural microorganism diseases. The composite microorganism viable bacteria preparation can effectively decompose a large amount of putrescent organic matters, inhibit the growth of harmful microorganisms and eliminate peculiar smells, and has the characteristics of high ammonia nitrogen removal rate, no generation of residual sludge, effective deodorization, low cost and the like.