Background and aims <p>The elevational distribution of microbial communities in the surface soils of natural lake wetlands has been widely studied. However, it remains unknown whether microbiota-mediated carbon metabolism in different soil layers exhibits a similar change pattern with elevation.</p> Method <p>In this study, we analyzed changes in functional genes that regulate carbon cycling in different soil layers and elevations using metagenomic analysis in Poyang Lake, China.</p> Results <p>The genes associated with the carbon cycle, particularly those involved in extracellular and intracellular carbon decomposition, are more abundant in surface soil (0–20&#xa0;cm) than in deeper soils (40–60&#xa0;cm and 80–100&#xa0;cm). The impact of elevation on the soil carbon cycle in wetlands varies across different soil layers. In surface soil, only a gradual increase in the abundance of methane oxidation genes with increasing elevation was observed. In deeper soils, the abundance of fermentation (formate, lactate metabolism) and anaerobic carbon fixation genes decreased with elevation, while methane oxidation (<i>mmo</i>, <i>pmo</i>) and CO oxidation (<i>coxMLS</i>) genes exhibited opposite trends. As soil depth increased, the genes involved in the soil carbon cycle exhibited stronger interrelationships and network complexity, and a greater number of carbon cycle genes showed a strong correlation with soil organic carbon. Furthermore, surface soil organic carbon was primarily influenced by plant characteristics.</p> Conclusions <p>Our findings suggest that microorganisms, rather than plants, play a crucial role in deep soil carbon storage and transformation.</p> Graphical Abstract <p></p>