The invention discloses a microbial enhanced oil recovery method and belongs to the technical field of tertiary oil recovery. The method is characterized by comprising the following steps: 1, conducting displacement of reservoir oil through biosurfactant; 2, adjusting injection-production patterns; 3, conducting displacement of reservoir oil through indigenous microorganisms; 4, conducting oil recovery through microorganism single well huff-and-puff. According to the method, firstly, the biosurfactant is injected, so that the displacement efficiency of a water-driven oil reservoir is improved; then through adjustment of the injection-production patterns, the swept volume, in the oil reservoir, of the indigenous microorganisms is expanded; finally, through the microorganism single well huff-and-puff treatment, crude oil in the immediate vicinity of an oil well is displaced out, and thereby the purpose of further raising the recovery ratio of the oil reservoir is achieved finally. The method has the advantages that activator has the advantages of being wide in source, low in price and harmless to strata; the method is wide in oil reservoir application range and particularly suitable for an oil reservoir which is exploited in a water-driven mode and is medium and high in permeability; the process is simple, and the pertinence and operability are great; the field test effect is good, and the enhanced oil recovery rate is testified by field tests to be larger than 15.0%. Therefore, the method can be widely applied to the technical field of microbial enhanced oil recovery.