Heterotrophic ammonia assimilation (HAA), a cutting-edge technology for high salinity wastewater treatment, faced a potential resistance challenge under Cr (VI). This study investigated the suppressive effects and self-restoration mechanisms under different stress levels of Cr (VI). The removal efficiencies of NH4+-N and Cr (VI) in HAA gradually decreased with higher influent Cr (VI) concentrations, with 20 mg/L marking the resistance threshold. Exposure to Cr (VI) led to an increase in high-molecular-weight proteins in soluble microbial products, concurrently stimulating the generation of extracellular polymeric substances. Heterotrophic functional microorganisms with Cr (VI) tolerance were enriched, such as Marinobacter and Planktosalinus. Assimilation pathway gene (glnA) and resistance genes (atoB) were up-regulated. After ceasing Cr (VI) addition, HAA system could increase the removal rate of NH4+-N by 17.12% due to its self-recovery ability. This study provided a scientific theoretical basis for HAA process to resist the impact of heavy metal-containing wastewater and self-recovery.