Available information on passivation effect of biochar on heavy metals (HMs) through regulating bacterial communities remains limited. Thus, this study investigated the correlation between bacterial diversity and HM-fractions (Zn, Cu, Cd, Cr and Pb) during composting with different dose of biochar (5% and 10%, dry weight basis), in order to ascertain the passivation effect on HMs under the influence of bacterial community. The addition of 10% biochar showed better passivation effect with reduction in bioavailability factor (BF) of Zn, Cu, Cd and Pb by 4.10%, 44.12%, 18.75% and 30.06%, respectively. In addition, it brought forward the variation in primary bacterial phylum to the thermophilic phase. The results of redundancy analysis (RDA) and structural equation models (SEMs) indicated that C:N ratio was an important factor in controlling the morphological transformation of HM by affecting the bacterial community structure. Our results maybe provide a novel insight into HM-passivation from an interaction mechanism on C:N ratio and bacterial community.