The application of organic materials contributes to the sustainable development of agriculture. Increased manure inputs have a fundamental effect on the composition and dynamics of soil organic carbon (SOC). In this study, we conducted a 10-year field experiment in Changchun, Jilin, Northeast China, to investigate the effects of manure addition on soil organic carbon components and soil microorganisms. Specifically, we established four treatments: (i) chemical fertilizer or no addition of manure (CK), (ii) pig manure with chemical fertilizer (ZF), (iii) cow manure with chemical fertilizer (NF), and (iv) chicken manure with chemical fertilizer (JF). The results showed that the JF treatment significantly increased the soil organic carbon (SOC), dissolved organic carbon (DOC), and readily oxidized organic carbon (ROC) content by 20.36%, 105.9%, and 61.32%, respectively, relative to CK. The microbial biomass carbon (MBC) content in JF, ZF, and NF treatments were significantly higher than that of CK, which increased by 107.24%, 116.45%, and 96.71%, respectively. The particulate organic carbon (POC) content in NF and JF treatments differed significantly, increasing by 25.61% and 19.01%, respectively, relative to CK. Redundancy analysis showed that continuous manure application had a positive effect on soil microbial community diversity and abundance, which was favorable for the accumulation of soil carbon. We also found that soil fungi were more sensitive than bacteria to changes in soil carbon composition following manure application. In conclusion, adding different organic materials can better support biodiversity conservation and realize ecosystem services of surface carbon storage and soil conservation. Our results reveal the importance of microbial fixation in soil carbon dynamics according to the different distribution of active organic carbon pools, which will help enhance our understanding of the carbon cycle.