Manure-compost-soil is the main pathway for the use of agricultural livestock waste. Biochar, regarded as the conditioner, was beneficial to nitrogen fixation during aerobic composting, and was to the enhancement of soil organic matter (OM) and nitrogen content, when applied with compost to the soil. But, the manure-compost-soil process was also related to microbial succession, whether biochar could affect this succession was not studied. In this paper, we investigated the influence of biochar on the manure-compost-soil process and its microbial community succession. Compared with the control group, biochar increased the OM and total nitrogen content of the compost. Biochar, compost and biochar-based compost improved the total carbon (TC) and OM of the soil. The genera of the initial composting sample were Saccharomonospora, Atopostipes and Lactobacillus, and were eliminated after high-temperature fermentation. Lysobacter, Glutamicibacter and Streptomyces were the dominant genera in the soil samples, promoting plant growth. Nocardiopsis, Saccharomonospora, Bacillus and Oceanobacillus dominated the genera in the whole manure-compost-soil process. Thus, aerobic composting could eliminate the toxic or negative bacteria that were directly input into the soil by manure. Those genera from compost or biochar-based compost flux into the soil could make an important contribution to OM’s cycle.