Geothermal systems represent discrete and relatively homogenous habitats for extremophiles; investigation into the microbial community is key to revealing the geochemical environment and the geochemical evolution of fluids in geothermal reservoirs. The reservoir of the Lindian geothermal field in Northeast China, is highly reducing and rich in methane, but the pathways of methane generation and the related microbial community structure are still unclear. In this research, five thermal water samples were collected and tested, and the microbial community structure and diversity were analyzed. The results show that in the sandstone reservoir belonging to the low-temperature (reservoir temperature < 90°C) brackish water (total dissolved solids concentration between 1000 and 10,000 mg/L) environment, the richness of the microbial community is relatively high. The microbial community structure is different from other geothermal systems reported but similar to that of oilfields, which may be related to the highly reducing geochemical environment with abundant organic matter. According to the analysis of archaeal function, the biogas production in the Lindian geothermal field is dominated by hydrogen nutrition type methane production, while the H₂ reducing methylamine type methane production is secondary, and results of Pearson correlation show that the archaeal communities are more strongly correlated to physicochemical factors than the bacterial communities.