The invention relates to a micro-capsulated suspended microbial seed coating agent and a preparation method thereof. The micro-capsulated suspended microbial seed coating agent comprises a functional bacteria microcapsule and auxiliaries, wherein the functional bacteria microcapsule is prepared from wall materials such as sodium alginate and gelatin by virtue of an endogenous emulsion process, the grain size of the microcapsule is 20-60 mu m, the content of functional bacteria is not lower than 10<9>cfu/g, and the embedding rate is over 80%. Functional microbes are selected from two or more of pseudomonas, bacillus subtilis, bacillus amyloliquefaciens, enterobacter cloacae, raoultella planticola and bacillus atrophaeus. The auxiliaries comprise one or more of a film-forming agent, a dispersant, a tackifier, an anti-freezing agent and a coloring agent. The prepared functional bacteria microcapsule is uniformly mixed with the auxiliaries to obtain a finished product. The product has the advantages of good film-forming performances, thallus persistence, high survivability, good slow-controlled release, strong application stability, environment friendliness, convenience in use, and the like, can be used for promoting seed germination and seedling growth of cottons, soya beans, wheat and potatoes, and the like, controlling the diseases at the seedling stage, improving stress resistance, and the like.