Rhizodeposition plays an important role in soil carbon (C) cycling, and the process of rhizodeposition-C transfer and conservation in soil has been considered to be mainly regulated by microbes. In this study, a pulse labeling approach combined with 13C-phospholipid fatty acids (PLFA) and 13C-nuclear magnetic resonance (NMR) techniques were used to test how the recently synthesized photosynthate-C was sequestered into soil by microbial processes during two growth stages of maize (Zea mays L.) under field conditions. The results showed that saprophytic fungi were important in the incorporation of labeled C at the vegetative stage, while actinomycetes were dominant at the reproductive stage. Additionally, the contribution of labeled C fixed in microbial biomass C (13C-MBC) to the total labeled C fixed in soil organic C (13C-SOC) increased from 5% at the vegetative stage to 25% at the reproductive stage, although the amount of 13C-MBC was almost the same at both growth stages. The difference in soil C chemical composition between vegetative and reproductive stages was primarily revealed in aryl C and O-alkyl C, with a higher proportion of aryl C at the vegetative stage and a higher proportion of O-alkyl C at the reproductive stage. Furthermore, saprophytic fungi and actinomycetes were linked to the higher proportions of aryl C and O-alkyl C in SOC at respective maize growth stages. Our results highlight the important role of soil microbes in the continuous processing and sequestration of rhizodeposition-C into the soil during the growth of maize. Further research should pay more attention to the microbial processes involved in the formation of SOC in different crop species and management practices under field conditions to clarify the importance of rhizodeposition for C sequestration and soil fertility.