In this study, the influence of coconut shell biochar addition (CSB) on heavy metals (Cu and Zn) resistance bacterial fate and there correlation with physicochemical parameters were evaluated during poultry manure composting. High-throughput sequencing was carried out on five treatments, namely T1−T5, where T2 to T5 were supplemented with 2.5%, 5%, 7.5% and 10% CSB, while T1 was used as control for the comparison. The results of HMRB indicated that the relative abundance of major potential bacterial host altered were Firmicutes (52.88–14.32%), Actinobacteria (35.20–4.99%), Bacteroidetes (0.05–15.07%) and Proteobacteria (0.01–20.28%) with elevated biochar concentration (0%−10%). Beta and alpha diversity as well as network analysis illustrated composting micro-environmental ecology with exogenous additive biochar to remarkably affect the dominant resistant bacterial community distribution by adjusting the interacting between driving environmental parameters with potential host bacterial in composting. Ultimately, the amendment of 7.5% CSB into poultry manure composting was able to significantly reduce the HMRB abundance, improve the composting efficiency and end product quality.