Soil organic carbon (C) is a critical component of terrestrial ecosystem C pools, playing a vital role in maintaining soil fertility, supporting sustainable agricultural development, and mitigating global climate change. Therefore, a comprehensive understanding of the pathways and effects of straw return and organic fertilizer application on soil C sequestration is essential. Straw return introduces exogenous C inputs that stimulate microbial activity and promote the formation of stable organic C fractions, although its decomposition is initially constrained by nitrogen (N) limitation. In contrast, organic fertilizer provides readily available stable C sources and essential nutrients, thereby enhancing soil aggregation and C stabilization. The combined application of straw return and organic fertilizer produces significant synergistic effects on soil C sequestration. Organic fertilizer alleviates microbial N deficiency caused by the high C to N ratio (C/N) of straw, facilitating more efficient straw decomposition and nutrient release. Simultaneously, it improves the functional structure of soil microbial communities, promoting the formation of mineral-associated organic C and strengthening aggregate-protected C pools. This integrated management strategy enhances short-term nutrient cycling while contributing to long-term C sequestration, offering substantial potential for advancing sustainable agriculture and climate change mitigation. This review aims to provide a theoretical basis for addressing the microbial mechanisms underlying the synergistic effect of straw returning to the soil and organic fertilizer application.