Cellulose can reduce endogenous ammonia production of non-ruminant animals by altering intestinal microbiota structure. Although the utilization of cellulose in fish is limited, we speculate that cellulose has a potential role in regulating fish ammonia tolerance. Four experiment diets with different cellulose levels (Ctrl, 4.00%, 6.00% and 8.00%) were formulated and fed to yellow catfish for 84 days. This study found that dietary supplemented with 6.00% cellulose can improve growth performance (final body weight and weight gain rate), blood health (total protein, albumin and globulin), intestinal digestive enzyme activity (protease, lipase and cellulase), and ensure intestinal structure integrity (villi length), and maintain intestinal microbiota stability (Shannon and Chao1 indexes). After 96 h ammonia stress, serum ammonia content and cumulative mortality were negative correlated with Cetobacterium abundance. The activities of ammonia metabolism enzyme (glutamine synthetase, carbamyl phosphate synthetase, argininosuccinic acid synthase and arginase) and antioxidant enzyme (superoxide dismutase, catalase and glutathione peroxidase) in 4.00% and 6.00% cellulose groups were higher than those in Ctrl and 8.00% cellulose groups. The highest mRNA expression levels of antioxidant-related genes (Cu/Zn-SOD, CAT, GPX and GR) and inflammation-related genes (IL1, IL 8 and TNFɑ) were found in 8.00% cellulose group. This study indicates dietary supplemented with cellulose can increase the Cetobacterium abundance in intestinal tract, which is closely related to ammonia tolerance of yellow catfish. The levels of 4.00–6.00% cellulose in dietary is recommended in juvenile yellow catfish.