Taking actual gravity-flow trunk sewers as research objects, this study adopted metagenomic technology to explore microbial mechanism underlying pollutant attenuation during wastewater transportation. The results show that along sewer flow direction, relative abundance of organic matter-degrading bacteria and denitrifying functional bacteria increases continuously, while that of nitrifying functional bacteria remains at a low level. Microorganisms in upstream section preferentially degrade simple carbon-containing organic compounds, and those in downstream section gradually decompose complex carbon-containing organics such as fatty acids. This metabolic process is mainly powered by glycolysis and tricarboxylic acid cycle. The progressively enhanced denitrification along sewers is primary cause for decline of nitrogen-containing pollutants. In addition, adverse slope at sewer end leads to enrichment of methanogens and related functional genes. Methanogenesis of organic matters further decreases content of carbon-containing pollutants. According to above mechanisms, optimizing operational parameters of wastewater treatment plants,regularly monitoring and removing sewer sediments, and reconstructing adverse slope sections can mitigate biodegradation of pollutants during wastewater transportation and effectively raise influent pollutant concentration of wastewater treatment plants.