The invention discloses a composite microbial agent and a preparation method and application thereof. The composite microbial agent includes a pseudomonas preparation, an acinetobacter preparation, a bacillus amyloliquefaciens preparation, a bacillus subtillis preparation, a bacillus licheniformis preparation, a pediococcus acidilactici preparation, a rhodobacter sphaeroides preparation, an alkali-lake dietzia preparation and a rhodopseudomonas palustris preparation. The preparation method includes the following steps that 1, composite microbial agent components are prepared; 2, the composite microbial agent components are mixed in proportion to obtain the composite microbial agent. The composite microbial agent can simultaneously decompose different organic matter, degrade amino nitrogen and nitro nitrogen in water, reduce phosphorus concentration in the water body and inhibit the growth of algae. The composite microbial agent is used for urban-rural sewage in-situ remediation, has the advantages of being high in efficiency, quick to take effect, free of no secondary pollution, simple in operation and the like, and large-scale application and popularization are facilitated.