The success of bio-technological processes for oil recovery depends on adequate understanding of the relationship between the microbial community structure and oil reservoirs conditions. This study was performed to identify the microbial community structures in 10 different types of water-flooded oil reservoirs on Sinopec Shengli Oil Field. These 10 oil reservoirs have a temperature at 55–91 °C, salinity at 3000–20000 mg/L, and permeability ranging at 207×10−3~6900×10−3 μm2. Some important rules were found that very rich diversified bacteria and archaebacteria were identified in the oil reservoirs, these microbial organisms have functions in hydrocarbon-degrading, production of active surfactants and methanogenesis which are very valuable properties required for displacement of oil, and the microbial community structures were affected by temperature, mineralization, permeability and water displacement factors in the oil reservoirs. More abundant archaebacteria and thermophilic bacteria (Thermus, Thermincola, Thermanaeromonas) were found in high-temperature oil reservoirs. In the oil reservoir with temperature above about 90 °C, the content of thermophilic bacteria was as high as 23%, and additionally a hyperthermophilic archaea, such as Geoglobus, was also identified in the microbial community. In oil reservoirs with salinity up to 10000 mg/L, halophilic bacteria content was 30%, which is twice as much as the reservoirs at lower salinity levels. In high salinity reservoirs, the strictly obligate anaerobic and denitrifying bacteria were not the predominant species. High permeability viscous oil reservoirs after long period of water injection resulted in significant increased microbial diversity by doubling species and genera number of microorganisms.