The invention belongs to the technical field of sewage treatment, and discloses a compound microorganism water purifying agent and an application thereof. The compound microorganism water purifying agent comprises a microorganism and a carrier, the microorganism comprises clostridium, saccharomycetes, micrococcus, acidobacteria, bacteroid, rhizobia, burkholderia cenocepacia, thiobacillus, opitutae, hydrogenophilales, lysobacter, brevundimonas, xanthomonas, comamonas, rhodocyclus and rhodospirillum, and the microorganism is fixed onto the carrier. The compound microorganism water purifying agent has high activity and is high in treatment efficiency, long-time domestication and selection is omitted, a short stable period is achieved in a treatment system, strains in the compound microorganism water purifying agent are cooperatively interact, utilization and metabolic decomposition of nutrient substances in water by the microorganism are facilitated, and COD (chemical oxygen demand) and ammonia nitrogen are efficiently reduced.