The return of straw and manure to agricultural fields can impact soil organic carbon (SOC) and biological properties. However, there is a lack of research on how to use swine manure, maize straw, and various conditioners together affects soil bacterial and fungal populations. This study aimed to investigate six treatments, namely, only maize straw (S00), maize straw combined with swine manure (S0Z), maize straw combined with biochar and swine manure (SCZ), maize straw combined with boron slag and swine manure (SBZ), maize straw combined with biological agent and swine manure (SJZ), and maize straw combined with bio-organic fertilizer and swine manure (SFZ). The results showed that after the two-year return, all treatments increased the SOC content in 2023, which was 12.55–26.89% higher than S00. And the SCZ treatment significantly increased the soil organic carbon (SOC), dissolved organic carbon (DOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and microbial biomass carbon (MBC) content by 26.89%, 25.44%, 56.88%, 16.08%, and 43.54%, compared to S00. A redundancy analysis (RDA) showed that the continuous application of manure, maize straw, and conditioners has a positive impact on the diversity and abundance of soil microbial communities, enhancing the accumulation of soil carbon. Furthermore, our research revealed that soil fungi exhibited higher sensitivity in soil carbon composition following the addition of manure, straw, and conditioners to agricultural fields than bacteria. In conclusion, the addition of different conditioners to the fields is beneficial to biodiversity conservation from the perspective of achieving soil carbon storage and soil protection. Our findings suggested that the combination of maize straw, biochar, and swine manure was been proven to be the most effective treatment for increasing labile organic carbon fractions and enhancing the microbial community.