In the context of global efforts to reduce carbon emissions, several studies have examined the effects of agricultural practices like straw returning and fertilization on the sequestration of carbon by microorganisms. However, our understanding of the specific microbial groups and their roles in long-term carbon increase remains limited. Therefore, we conducted a 36-year farmland experiment (1984–2020) to investigate the impact of bacterial carbon metabolism on the augmentation of soil organic carbon. Our findings demonstrated a noteworthy increase in the diversity of microorganisms in farmland as a result of long-term straw returning and the application of mixed chemical fertilizers. However, when we examined the functions of farmland microorganisms involved in carbon metabolism, we observed that the effects of fertilization on carbon metabolism were relatively consistent. This consistency was attributed to a deterministic competitive exclusion process, which minimized differences between treatment groups. On the other hand, the influence of straw addition on carbon metabolism appeared to follow a more random pattern. These changes in microbial activity were closely linked to the down-representation of core metabolic pathways related to carbon metabolism. Notably, long-term fertilization had a negative impact on soil organic carbon levels, while long-term straw fertilization resulted in a positive increase in soil organic carbon. These findings have important implications for enhancing soil organic carbon content and grain yield in regions with typical black soil characteristics.