Exercise can have beneficial effects on fish. However, there is few studies on the expression profile analysis of muscle growth regulation genes and impact of water flow stress on expression levels of the muscle genes in fish. In this study, myogenic regulatory genes (MyoD), myostatin-regulated genes (Mstnb), myoblast development-related genes (Desmin and MYHC) were displayed high expression in muscle tissues of adult zebrafish. MyoD, MyoG, MRF4 and MYHC are higher expression at the muscle effect stage embryos. And we explore that the 30 days old is critical muscle growth period in zebrafish. Furthermore, water flow stress can enhance the expression levels of myogenic regulatory factors (eg. MyoD, MyoG) and myoblast development-related genes (Pax7, Desmin) in the zebrafish trunk dorsal muscle, while the mRNA levels of myostatin regulatory genes, such as Mstna and Mstnb, are significantly down-regulated. Our results suggest that appropriate water flow stressing for 1–2 weeks could promote zebrafish muscle growth, while zebrafish may be in motor fatigue after four weeks of water flow stress. This research provides a foundation for further exploration of fish exercise physiology and adaptation, and is significant for fish farming and conservation.