Acidic fluids produced by microbial metabolism, such as organic acids, can effectively increase the porosity and permeability of carbonate rocks, thus improving oil recovery. In this experiment, facultative anaerobic strains utilizing crude oil as the sole carbon source were screened out. Acid production from crude oil was determined, and their physiological and biochemical properties and gene expression under the influence of salinity degree were studied. A core experiment simulation was performed to explore the effects of the selected microorganisms on the permeability and porosity of the reservoir. The results showed that the isolated microorganism was Bacillus licheniformis. Microbial growth was excellent when the salinity was 2 x 10(4) mg/L. The acid production concentration reached 380 mg/L. The transcriptome test revealed that compared with the 1 X 10(4) mg/L salinity degree, 2 X 10(4) mg/L salinity changed 106 genes, of which 69 and 37 were up and downregulated, respectively. The functional annotation of differential genes was performed by GO enrichment. The differential expression of GO:0015940 and GO:0015939 is a biological cause that affects microbial oil recovery effect. The expression of these differential genes may be the root cause of microbial effects. The results of simulated flooding experiments show that the selected oil removing bacteria can increase oil recovery by about 7.3%. This study provides theoretical support for the microbial enhancement of carbonate recovery from a microscopic perspective.