Studying the effects of microorganisms on the decomposition of litter and its action law are great significance for revealing the changes of ecosystem material cycle and ecological function. In this study, the dominant lakeside plants Zizania latifolia and Hippuris vulgaris were used as the research objects from the Napahai wetland, which is located on the Northwestern Yunnan Plateau. The mass attenuation characteristics and changes in microbial carbon source utilization and metabolism of litter under different interfaces were studied by Biolog GenⅢ identification technology. The results revealed that: (1) after oneyear decomposition, the mass residue rates of Z. latifolia at air interface, water interface and soil interface were 77.7%, 42.2% and 25.3%, respectively, which were significantly higher than those of H. vulgaris (41.6%, 32.5%, 12.4%). For the same species, the mass residue rates at different decomposition habitats were air interface > water interface > soil interface. (2) There is a difference in the AWCD values of the two plants at different interfaces. The microbial carbon source has the highest metabolic intensity at the soil interface for Z. latifolia and the air interface for H. vulgaris. Microbial carbon source utilization of Z. latifolia was the highest under soil interface, and carbon source utilization of alcohols and amines reached 0.26 and 0.24, respectively. (3) There are certain differences in the microbial community structure between two plant litters. The microbial community at the soil interface of Z. latifolia litter has a strong ability to utilize all kinds of carbon sources, and its microbial community contains abundant species, and its community uniformity and diversity are more obvious, which is consistent with the seasonal variation of Z. latifolia mass residue rate. To study the relationship between the decomposition of litter and microorganisms can provide scientific basis and reference for the stability and development of ecosystem and the microbiological mechanism of litter decomposition.