Soil organic carbon (SOC) is the largest terrestrial carbon pool that can provide nutrients to plants. Intercropping is a sustainable agriculture method with appreciable potential to improve crop productivity and enhance SOC pools and mitigate soil degradation. However, the inconsistent findings generated by on-site experiments necessitate a comprehensive assessment of how intercropping affects SOC. To address this gap, we conducted a meta-analysis to assess the effect of intercropping on SOC. The data was collected through Web of Science, Scopus, and China National Knowledge Infrastructure (CNKI). The results showed that the SOC content of intercropping was 17.75 % higher than that of monocropping. The crop composition and depth of the soil layer were identified as the main factors affecting the accumulation of SOC. Further, the presence of legume crops is not necessary to promote SOC accumulation, and intercropping contributes to SOC accumulation in the 0–20 cm soil layer. Soil total nitrogen (TN), soil microbial carbon (MBC), soil microbial nitrogen (MBN), and the soil carbon/nitrogen (C/N) ratio are positively correlated with SOC accumulation, while soil microbial diversity and enzyme activity are negatively correlated with SOC accumulation. The advantage of SOC accumulation in intercropping is lost when the soil C/N ratio is higher than 10.79 compared to monocropping, and intercropping has a higher potential for SOC accumulation when the MBC is higher than 182.92 mg·kg–1. The SOC accumulation potential of intercropping is greater than that of monocropping when soil bacterial diversity is greater than 6.55. Thus, SOC accumulation in intercropping is affected by crop composition and depth of soil layer, and regulated by soil C/N ratio and microorganisms, especially in soil with low N or low C/N ratio.