based on the reservoir condition of the second plant of DaQing oilfield after waterflooding，microbial enhanced oil recovery experiment was developed，and the Indigenous microbial strains Rhodococcus rubber（Rr）with better emulsification was selected，and its physiology and biochemistry characteristic were studied，the saturated hydrocarbon compositions of the crude oil before and after biochemical reaction were analyzed，and the changes of the indigenous microorganism and metabolites were measured with the physical model；the microbial flooding experiments were conducted. The results showed that Rr had better emulsification to oil and paraffin，the emulsification activity of oil-water interface was higher than 60%；the saturated hydrocarbon concentration of nC₁₁—nC₁₇ decreased after microbial reaction；no Rr was checked from the liquid of physical models during incubation；acetic acid，propionic acid，propanedioic acid，citric acid，succinic acid，etc，were evaluated with liquid chromatography， and the concentration of acetic acid was up to 166.19 mg/L. The results of microbial displacement experiment showed the air injection could not enhance oil recovery effectively，the injection of excessive Rr could disturb the Microorganisms' ecological equilibrium，and the simple injection of mineral medium could activate the Microorganisms well and obtain higher enhancement of oil recovery（8.51%）. Accordingly，indigenous microbial flooding after water flooding was suggested in the second plant of Daqing oilfield.