The invention relates to a composite bacterial agent for deodorization and a preparation method thereof; the composite bacterial agent comprises a bacillus group composed of bacillus subtilis, thiobacillus intermedius, bacillus licheniformis, and a yeast group composed of saccharomyces ellipsoideus and nectaromyces sp. The preparation method comprises the following steps: activating the purchased2 groups of microorganism, preparing a bacterial agent with a total colony count of each group of not less than 1*107/ml by two steps of seed culture and fermenter culture, uniformly distributing the2-group bacterial agents at different areas of fillers in a biological filter tank for deodorization operations, wherein the bacterial agent comprises by weight 30-50% of bacillus groups and 50-70% of yeast groups, and the two groups are not mixed during distribution. The composite bacterial agent for deodorization prepared by the method provided by the invention has the advantages of good deodorization effect and long deodorization period, and the service time is increased by above 30% when compared with that of agents without the addition of the composite bacterial agent.