The pretreatment process is often unable to completely intercept heavy metals in wastewater, facing a huge risk of leakage, increasing the difficulty of treating pollutants in the subsequent biochemical process or even leading to the collapse of the system, and facing the difficulty of inoperability and rehabilitation. Heterotrophic ammonia assimilation has the potential to maintain some stability after heavy metal shock, thanks to its rapid microbial proliferation, robust resistance to high loads, remarkable environmental adaptability, and inherent stability. Bio-accelerators dosing strategies could strengthen the performance recovery ability of traditional bio-system after heavy metal impact. However, no recovery strategies for inhibiting HAA have been reported. Herein, three bio-accelerants, specifically, vitamin A, 6-benzylaminopurine, and α-ketoglutaric acid, were investigated for their potential to restore the HAA system impacted by 20 mg/L Cr (VI). The three bio-accelerants effectively mitigated the toxicity of the HAA system, resulting in a 60.4% increase in NH4+-N removal efficiency within just 6 days with cytokinin. During toxicity remediation, three bio-accelerants facilitated the production of extracellular protein components in soluble microbial products and stimulated the secretion of extracellular polymeric substances. The three bio-accelerants enhanced competition among genera and influenced community assembly processes to regulate community structure and enhance functional gene expression. This study offers a practical approach to enhancing the HAA process and remediating microbial toxicity.