The mechanism of immobilization of heavy metals in the soil using biochar has been studied extensively. However, the decomposition of biochar by biological and abiotic factors can reactivate the immobilized heavy metals in soil. Previous research showed that the addition of biological calcium carbonate (bio-CaCO3) can significantly increase the stability of biochar. However, the influence of bio-CaCO3 on the ability of biochar to immobilize heavy metals remains unclear. Therefore, this study evaluated the effect of bio-CaCO3 on the use of biochar to immobilize the cationic heavy metal lead and the anionic heavy metal antimony. The addition of bio-CaCO3 not only significantly improved the passivation ability of Pb and Sb but also reduced their migration in the soil. Mechanistic studies have shown that the reasons for the enhanced ability of biochar to immobilize heavy metals can be summarized in three aspects. First, the introduced inorganic component CaCO3 can precipitate and exchange ions with lead and antimony. Second, the N element in the organic component of bio-CaCO3 underwent polycondensation with the organic carbon in biochar to form pyridine N and pyrrole N structures, which can form a strong complex with lead and antimony. Pyridine N complexes more strongly than pyrrole N. Third, bio-CaCO3 increased the degree of aromatization and the surface π-electron density of biochar, which enhanced the ability of biochar to adsorb heavy metals. This study will provide a new concept for the application of biochar as an amendment to remediate heavy metals in the soil.