Indigenous microbial enhanced oil recovery (IMEOR) has been successfully applied in conventional oil reservoirs, however the mechanism in low-permeability oil reservoirs is still misunderstood. In order to profile the role of indigenous microcosms in oil recovery, the phylogenetic diversity of the microbial community inhibited in the reservoir by stimulation with optimized nutrients in vitro were investigated by MiSeq platforms sequencing 16S rRNA gene amplicons. Results showed that the microbial community after stimulation was dramatically changed and an increasing abundance of functional microorganisms with the ability to producing biogas, biosolvent and biosurfactant was clearly detected under anaerobic conditions: such as the genus of Clostridium, Bacillaceae, Enterobacteriaceae, Oleomonas, Marinobacter, Pseudomonas, Marinobacterium and Dietzia. Core flooding tests within sandstone were implemented and indicate that these enriched microorganisms were closely related to incremental oil recovery. In particular, biogas-producing bacteria made the most significant contribution with obvious evidence of a pressure increase during the core flooding test with no observation of decreasing surface tension and emulsification. These results suggest that the stimulation of indigenous biogas producers is a promising strategy for improving oil recovery in low-permeability oil reservoirs.