In order to study the influencing mechanism of sulfur oxidizing bacteria on the mortar in sewage, the microbial metabolic process and the macro and micro performance of the mortar was analyzed by chromatography, ultra depth microscope, scanning electron microscope and other methods. The results show that metabolism of sulfur oxidizing bacteria can convert sodium thiosulfate to biological sulfate instead of biological sulfuric acid. Compared with the influences of sterilized sewage medium, the sulfur oxidizing bacteria have a corrosion inhibitory effect on the performance of the mortar. The surface of the specimens of test group with sulfur oxidizing bacteria is attached with biofilms, which have a complex microstructure and many holes, and the biofilms can accumulate a large number of sulfur oxidizing bacteria to generate SO2-4, which can target the surface of the mortar.