The influence of copper ion (Cu2+) on anaerobic ammonium oxidation (anammox) performance and microbial community structures after oxytetracycline (OTC) stress recovery were assessed. Experimental results demonstrated that anammox performance were stressed by 1.0 mg L−1 Cu2+ and inhibitions were reversible with total nitrogen removal rate higher than 3.08 ± 0.2 kg N m−3 d−1. The residual OTC in the anammox sludge could combine with Cu2+ introduced and thereby retarded inhibition on performance in the presence of 2.0 mg L−1 Cu2+. Moreover, the positive relation of dominant bacterium Ca. Anammoxoglobus with the abundance of functional genes and parts of antibiotic resistance genes were observed, suggesting that regain of performance was the results of the gradual domestication of latent resistant species after inhibition. This investigation reveals new insights into resistance of anammox performance for Cu2+ and OTC.