The appearance of heavy metals in wastewater brings a major burden to wastewater treatment plants, due to the high toxicity to microorganisms. Several commonly used heavy metals, including Zn(II), Cd(II), Hg(II), and Pb(II) were adopted to clear the individual and joint toxicity to the completely autotrophic nitrogen removal over nitrite (CANON) process in six sequencing batch reactors. The obtained results suggested that the nitrogen removal performances were transiently inhibited, but rapidly recovered. The restoration period under the stress of Hg(II) and Pb(II) was shorter than that under Zn(II), Cd(II), and the joint heavy metals. During the long-term exposure, Cd(II) in 1mg L −1 slightly inhibited the nitrogen removal, while Zn(II), Hg(II), Pb(II), and mixture showed a negligible impact on CANON process. The defense of extracellular polymeric substances (EPS), the good adaptability of functional bacteria, and the inducement of resistant genera by heavy metals all contributed to the robustness and stability of CANON process. Therefore, it is feasible to treat nitrogenous wastewater containing low heavy metals using CANON process.