Biochar and stover returned directly enhanced soil organic carbon (SOC), microbial biomass carbon:SOC, total amino sugar carbon, glucosamine carbon, galactosamine carbon, N-acetylglucosaminidase (NAGase) activity, and chiA gene abundance significantly. There were significant positive correlations between the abundance of the soil chiA gene and NAGase activity. Biochar and stover increased the number of total operational taxonomic units (OTUs), unique OTUs, and the chao 1 and ACE richness indices, but decreased the Shannon and Simpson diversity indices. Similar soil properties, diversity, and the abundance of chiA were observed between compost and stover-removing, or between biochar and Stover. Some detectable genera of chiA community in the biochar or stover plots was significantly different from that in the CK plots.