Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland, the results indicate that three samples have different physicochemical characteristics, their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1, mutually demonstrate the prominent role in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance genes and its emphatic research value for microbial resistance issues. The results above have preliminarily proved the indicator of soil microbial communities in predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change.