[Objective] The soil in the vegetable plantation suffered from fertility degradation, pH decrease, and heavy metal leaching, necessitating the exploration of the mechanism by which composite bacterial agents regulate the bacterial community structure, nitrogen composition, and heavy metal availability in the vegetable plantation soil. [Methods] The heavy metal-resistant bacterial strains Ralstonia Bcul-1 (R-B) and Bacillus cellulasensis Zn-B (BC-Z) were prepared with biochar as an immobilized bacterial agent and then applied to the acidic soil (pH 5.6) of a vegetable plantation under long-term tomato rotation. High-throughput sequencing of soil bacteria and the determination of soil composition were conducted to analyze the bacterial diversity, soil pH, nitrogen-carbon content, and heavy metal chemical speciation, on the basis of which the effects of the biochar composite bacterial agent on the bacterial community structure, nitrogen-carbon supply, and heavy metal activity in the soil were analyzed. [Results] Biochar immobilization facilitated the growth of exogenous bacteria R-B and BC-Z in the vegetable plantation soil contaminated with heavy metals and maintained long-term coexistence of R-B and BC-Z with the original highly resistant Bacillus (10.18%-11.88%) in the soil. Accordingly, it effectively improved the bacterial community structure, adjusted the distribution of differential bacteria (biomarkers), and restoratively increased the relative abundance of abundant bacteria (such as Streptomyces, Geopathophilus, and Nocardioids) in the soil. In addition, soil bacterial genera, partial abundant bacteria, and the exogenous bacterial strain R-B were closely related to heavy metal chemical speciation and nitrogen-carbon components. The application of biochar bacterial agents (BI+R-B, BI+BC-Z, and BI+R-B+BC-Z) increased the pH, EC, total nitrogen, nitrate nitrogen, organic matter, and total organic carbon of the soil by up to 0.41, 20.74%, 18.96%, 24.77%, 10.26%, and 21.56%, respectively, while decreasing the ammonium nitrogen residue by 13.91%, maintaining the nitrogen-carbon supply capacity of the soil. BI+R-B and BI+R-B+BC-Z reduced the content of exchangeable, reducible, and oxidizable heavy metals (Cd, Cr, Pb, Cu, and Zn) by 0.18%-12.33%, but increased the residual content of these heavy metals by 0.16%-14.59%, effectively passivating heavy metals in the soil. [Conclusion] The biochar composite bacterial agent (BI+R-B+BC-Z) improved the bacterial community structure, promoted R-B growth, increased the abundance of abundant bacteria, and maintained the long-term coexistence of exogenous bacteria R-B and BC-Z with the original highly resistant Bacillus in the vegetable plantation soil with heavy metal compound pollution. Moreover, it increased soil pH, EC, total nitrogen, nitrate nitrogen, total organic carbon, and organic matter, while reducing ammonium nitrogen residue and passivating soil heavy metals (Cd, Pb, and Cu). Therefore, it effectively regulated the bacterial community activity, exogenous bifunctional bacterial growth, nitrogen-carbon supply, pH, and heavy metal chemical speciation, with the potential to maintain the fertilizer supply capacity and control heavy metal compound pollution of vegetable plantation soil.