Changes on the muscle quality of Wuchang bream exposed to different ammonia nitrogen (AN) models during transportation were investigated. Upon AN stressing, fish gill apparently injured, resulting in the increases of ROS content, apoptosis rate, and adjacent gap of muscle cells, and the blurring of muscle fibers. These bio-physiologic changes depended on AN exposure model, e.g., concentration and time. Among different models, the fish exposed to high concentration AN (50 mg/ L) showed the highest drip loss and lowest shear force under short time (3 h) and long time (24 h), respectively. Lightness of the fish exposed to low concentration AN for long time was the highest, and the lowest yellowness for the one exposed to fluctuate concentration AN for long time. The mechanism on changes of muscle quality by AN exposure was mainly related to the upregulation of MAPK/p53, NF-κB and PI3K/AKT signaling pathways to modulate apoptosis.