Microorganisms in petroleum reservoirs mediate hydrocarbon degradation coupling with methanogenesis process as the terminal step, they also contribute to microbial enhanced oil recovery (MEOR) worldwide with great economic and environmental benefits. Here, a molecular investigation, using the 16S rRNA and mcrA gene profiles based on MiSeq sequencing and clone library construction method, was conducted on oil and water (aqueous) phases of samples with high, moderate and low temperatures from seven petroleum reservoirs in China. A core bacterial microbiome with a small proportion of shared OUT, but a high proportion of sequences among all reservoirs was discovered, including aerobic degraders, sulfate/nitrate reducing bacteria, fermentative bacteria and sulfur cycling bacteria distributed mainly in Proteobacteria, Bacteroidetes, Deferribacteres, Deinococcus-Thermus, Firmicutes, Spirochaetae and Thermotogae. Their prevalence in the reported petroleum reservoirs and successive enrichment cultures suggest their common roles and functions involved in aliphatic and aromatic hydrocarbon degradation. Dominant methanogenesis process generally shifts from hydrogenotrophic pathway in water phase to acetoclastic pathway in oil phase in high temperature reservoirs, but the opposite is true for low temperature reservoirs. No differences were detected between two phases in moderate temperature reservoirs. Physiochemical factors, including pH, temperature, phase conditions, and nitrate, Mn²⁺, and Mg²⁺ concentrations are the main ones correlating to the microbial compositional and functional profiles significantly. LEfSe analysis shows distribution differences of microbial groups towards pH, temperature, and oil/water. Tax4Fun functional profiling indicates major functional metabolism differences between the two phases, including amino acids, hydrocarbons in the oil phase, and carbohydrates in the water phase.