This study investigated the effects of elevated $CO_2$ and nitrogen addition on the anaerobic decomposition mediated by microorganisms to determine the microbial metabolic pathways in the degradation of organic matters of the sediments. There were statistically significant differences(P < 0.05) in the rates between denitrification and methanogenesis upon increased $CO_2$ concentration, nitrogen addition, in the presence of plants. Based on the assumption that anaerobic degradation of organic matter mainly occurs through denitrification, iron reduction, and methanogenesis, methanogenesis is the dominant pathways in the decomposition of organic matter under the condition of elevated $CO_2$ and nitrogen addition. In addition, the altered environment increased anaerobic carbon decomposition. Therefore, it can be concluded that freshwater wetland sediments have positive effects on the global warming by the increased methanogenesiss as well as increased anaerobic carbon decomposition.