The effects of divalent copper (Cu(II)) on microbial community, enzymatic activity and functional genes in a sequencing batch reactor (SBR) at tetracycline (TC) stress were investigated. The enzymatic activity and functional genes abundance associated with nitrification and denitrification at a 20 mg L−1 TC stress were higher than those at a mixtures stress of 20 mg L−1 TC and 10 mg L−1 Cu(II), while they were lower than those at a mixtures stress of 20 mg L−1 TC and 40 mg L−1 Cu(II). Compared to lactate dehydrogenase (LDH) release and reactive oxygen species (ROS) production at a 20 mg L−1 TC stress, they were lower at the TC stress with 10 mg L−1 Cu(II), while they were higher at the TC stress with 40 mg L−1 Cu(II). The incremental Cu(II) concentration at a 20 mg L−1 TC stress could not change the result that the sensitivity of denitrifying enzymatic activity to TC was higher than nitrifying enzymatic activity. Compared to the relative abundance of nitrifers and denitrifers at a 20 mg L−1 TC stress, the 10 mg L−1 Cu(II) addition resulted in their increase, while they decreased as the 40 mg L−1 Cu(II) addition. The relative abundance of genera Pseudomonas, Rivibacter and Nitrobacter at the stress of Cu(II) and TC were higher than those at TC stress, suggested they had an ability to resist the stress of Cu(II) and TC.