As an inevitable factor in aquaculture, ammonia plays a critical role in macrolide antibiotic resistance, leading to accumulating of antibiotic-resistant bacteria in fish skin mucus. In this study, four experimental groups were implemented to test the effects of ammonia alone or in combination with roxithromycin for 28 days on skin mucus microbial composition and the immune response of yellow catfish: CON (control), AN (50.00 mg L−1 total ammonia nitrogen, TA-N), ROX (100 μg L−1 roxithromycin), and HR (50.00 mg L−1 TA-N, 100 μg L−1 ROX). This study demonstrated that ammonia or roxithromycin exposure resulted in increased plasma ammonia content and decreased total antioxidant capacity. Compared with AN group, the combined exposure of ammonia and roxithromycin inhibited the skin mucus immune response. Microbial composition analysis showed that combined exposure of ammonia and roxithromycin had no significant effect on skin mucus α-diversity as compared with CON group. The abundance of Cetobacterium, Rhizobiales_Incertae_Sedis_uncultured and Acinetobacter was increased significantly with the combined effect of ammonia and roxithromycin, these bacteria may be potentially antibiotic-resistant. As compared with CON group, the combined exposure of ammonia and roxithromycin did not affect skin goblet cell counts. This study suggests that combined exposure to ammonia and ROX increases the risk of the emergence of antibiotic-resistant bacteria.