Long-term high intensity utilization leads to the degradation of black soil in Northeast China and the serious loss of organic carbon. Biochar has great potential for improving the carbon storage capacity of agroforestry ecosystems and reducing greenhouse gas (GHG) emissions. However, the effectiveness of biochar application depends on pedoclimatic factors, and few studies have explored the effects of biochar and its modified biochars on the net ecosystem economic benefit (NEEB) of black soil farmland. To increase the environmental benefits of carbon sequestration and emission reduction and to improve farmer profits, this study modified biochars by physical, chemical and biological methods, and studied the effects of different types of modified biochars on soil properties, crop yield and GHG emissions in black soil farmland through field experiments. The NEEB of different treatments was evaluated by combining carbon cost, yield benefit and biochar cost. A total of 6 treatments were used in the experiment: normal fertilization (CK), fertilization + raw biochar (BC), fertilization + physically modified biochar (PBC), fertilization + acid-modified biochar (HBC), fertilization + magnetically modified biochar (MBC), and fertilization+ biologically modified biochar (BBC) treatments. Compared with the control (CK), the application of biochar increased the content of soil organic matter by 18.76-42.57% and improved the soil fertility. The raw biochar had no significant effect on soybean yield and increased the global warming potential by 41.18%. Soybean yields significantly increased with decreasing GHG emission intensity when modified biochars were applied. Due to the high cost of biochar and the current low carbon price, the effect of biochar on crop yield is crucial for increasing the NEEB. The NEEB in the HBC treatment was the highest, 57.86% higher than that in the CK treatment and was an effective strategy for increasing crop yield while reducing GHG emissions. The results of this study could provide a theoretical basis and technical support for soybean farmland carbon sequestration, emission reduction, soil improvement and yield improvement in the black soil region of Northeast China.