This study aimed to explore a new way to address the burning of agricultural waste in China while achieving the sustainable use of it. Three agricultural wastes (Wheat straw, peanut shell, and rice husk) were slowly pyrolyzed into biochar, which was subsequently added to the soil to reduce CO2 emissions from the soil, and to improve soil fertility as well as microbial community structure. The biochar and raw materials were added to the soil and cultured under controlled conditions, and then the CO2 emissions produced from the mixing. At the same time, this study used pot experiments to determine the effects of biochar on tobacco soil physical and chemical properties and, therefore, the microbial communities of the soil. This study suggests that (1) biochar can effectively reduce soil CO2 emission rate. Compared with the control, peanut shell biochar could reduce the total CO2 emissions of soil by 33.41%, and the total CO2 emissions of wheat straw biochar treatment was 90.25% lower than that of wheat straw treatment. (2) The soil’s physical and chemical properties were improved. The soil bulk density of wheat straw biochar treatment kept 34.57% lower than that of the control as well as 21.15% lower than that of wheat straw treatment. The soil’s organic carbon of peanut shell biochar treatment was 87.62% more than that of peanut shell treatment. (3) Biochar changed soil microbial community structure. (4) Biochar is suitable for tobacco growth. Peanut husk biochar significantly increased the total biomass of tobacco, and wheat straw biochar significantly increased tobacco root vigor. This study concluded that processing Chinese agricultural waste into biochar and adding it to the soil instead of burning it directly would be an effective means to reduce greenhouse gas emissions, to improve soil, and to promote crop growth.