Shrub invasion affects plant growth and soil physicochemical properties, resulting in soil microbiota metabolic pathway changes. However, little is known about the shrub expansion intensity of microbial metabolic pathway processes. In this study, we used metagenome sequencing technology to investigate changes in soil microbial C and N metabolic pathways and community structures, along with different shrub invasion intensities, in the Sanjiang Plain wetlands. Different shrub invasion intensities significantly affected the soil microbial composition (β diversity), with no significant effect on the α diversity compared to CK. AN, pH, and TP were the major factors influencing the microbial community's structures. Compared to CK, the shrub expansion intensity did not significantly affect C fixation and central metabolism but significantly reduced methanogenesis, which involves the CO-to-methane transition that occurs in methane metabolism, and denitrification, the nitrite to nitric oxide (nirK or nirS) transition that occurs in N metabolism. This study provides an in-depth understanding of the biogeochemical cycles of wetland ecosystems in cold northern regions undergoing shrub invasion.