Intercropping can increase soil carbon (C) sequestration and utilization by planting a variety of plants on a same land. However, the main plant and microbial-driven pathways leading to the increased C sequestration in intercropping soils are rarely studied. Therefore, it is important to reveal the distinct contributions of plant- and microbe-derived C to soil organic C (SOC) for understanding the regulation of intercropping in global C storage. Herein, two widely accepted sets of bio-markers, namely, amino sugars and lignin phenols, were employed to compare the distribution of plant- and microbe-derived C as well as their contributions to SOC in maize monoculture and intercropping systems, based on a field experiment established in 2013; meanwhile, the associations of soil physicochemical properties and microbial physiological traits with plant- and microbe-derived residues were disclosed via correlation and model analysis. Compared with the monoculture, maize intercropping significantly increased soil amino sugar and microbial necromass C contents as well as their contributions to SOC in maize mature stage; maize inter-planted with gingelly or soybean significantly increased these variables in the elongation stage; meanwhile, maize inter-planted with gingelly significantly increased soil lignin phenol content and its contribution to SOC in the mature stage. In all treatments and growth stages, microbial necromass C contributed more to SOC than lignin phenols, and fungal necromass C contributed more to SOC than bacterial necromass. The contribution of microbial necromass C to SOC was mainly influenced by amino sugar content, microbial C use efficiency, dissolved organic C content, and microbial biomass C content. The contribution of plant-derived C to SOC was mainly influenced by lignin phenol content, pH, and NH4+-N content. These results demonstrate the distinct regulations of maize intercropping on plant- and microbe-derived C to soil C pool by influencing soil physicochemical properties and microbial physiological traits, and meanwhile, highlight the potential of intercropping in global C storage.