Abstract：In this paper, a microcosmic physical simulation system was established by transparent micro-model to study the mechanisms of Microbial Enhanced Oil Recovery (MEOR). Two hydrocarbon oxidizing strains (Rhodococcus ruber Z25 and Bacillus cereus Z31) were employed. The rules of water-flooding process and distribution of residual crude oil were obtained by water-flooding experiment. The main residual oil located in the surface and the blind zones of porous media in the form of constant oil phase. After the cultivation of the microorganisms, zoogloea was observed in the interface between aqueous and oil phase. The residual oil was incised into pieces and the structure of the oil was totally destroyed. Therefore, the post water-flooding had performed efficiently in displacing the residual oil due to the metabolic activities of the microorganisms. The main effects on EOR process and the oil-displacing mechanisms by hydrocarbon oxidizing bacteria were studied, which would contribute to the potential application of MEOR in the pilot test.