Purpose <p>This study aimed to elucidate the mechanism by which modified biochar (BC) ameliorates acidic soil and promotes soybean growth.</p> Methods <p>A pot experiment was performed using different types and application rates of BC, including unmodified BC, calcium carbonate-modified BC (MBC), and a mixture of BC and calcium carbonate (CBC). This study investigated how these BC types influenced pH, cation exchange capacity (CEC), the contents of soil exchangeable aluminum (Al³⁺), and further explored how they regulated root microbial communities to enhance the absorption of nitrogen by soybean roots.</p> Results <p>BC application (regardless of type) significantly increased soil CEC and soybean fresh pod weight while reducing the contents of soil exchangeable Al³⁺. Compared with the BC and the CBC, the MBC significantly increased soil pH, soybean nodule number, fresh pod weight, and grain nitrogen (N) contents. In terms of application rates, compared with 0.5%MBC, 1%MBC further increased soil pH, CEC, soybean root length, stem-leaf N contents, and the Chao1 index of root microbial communities, while significantly decreasing soil Al³⁺ content and root cell membrane permeability. Path analysis revealed that the increase in soil pH significantly promoted the Chao1 index of root microbial communities and the relative abundance of <i>Cyanobacteria</i>, which promoted root elongation and nodule formation, thereby enhancing nitrogen accumulation in grains and increasing pods number.</p> Conclusion <p>Calcium carbonate modified biochar can ameliorate soil acidity, regulate soybean root growth, and increase soybean pod number. Among the treatments, the 1% MBC application rate yielded the optimal results, making it a recommended amendment for acid soils in soybean production.</p>