The invention belongs to the technical field of sewage treatment, and particularly relates to a system and method for treating sewage by using microorganisms. The system comprises: a pretreatment unit, an anaerobic microorganism treatment unit, an aerobic microorganism treatment unit, and a biofilm filtration unit, wherein the pretreatment unit is used for sedimentation of suspended solids, insoluble organic matters, inorganic particles and other particles in the sewage, anaerobic microorganisms are used to further treat the sewage to degrade hardly degradable organic matters in the sewage through the anaerobic microorganism treatment unit, aerobic microorganisms are used to further treat the sewage to degrade degradable substances in the sewage through the aerobic microorganism treatmentunit, and a biofilm is used to filter the sewage treated by the above treatment units through the biofilm filtration unit. The efficient degradation of micro-pollutants in the sewage is realized through filtration of the microorganisms and the biofilm, the problem that residual micro-pollutants still exist in the water resource treated in the prior art is solved, a good and sustainable-operation sewage treatment system can be formed, and the effects of deodorization, decolorization, turbidity removal, nitrogen and phosphorus removal, and pollutant removal can be realized.