This study investigates the effect of a sudden change in salinity for 48 h on the digestive enzyme activity of juvenile yellowfin tuna. The treatment included a control salinity of 32‱ in natural seawater and an experimental salinity of 29‱. Acute stress experiments were carried out on 72 juvenile yellowfin tuna (646.52 ± 66.32 g) for 48 h to determine changes in digestive enzyme activity in different intestinal sections over time (0 h, 12 h, 24 h, 48 h). The activities of pepsin, trypsin, α-amylase, lipase, and chymotrypsin in the digestive organs (stomach, foregut, and pyloric ceca) of juvenile yellowfin tuna were measured. Pepsin and pancreatic protease in the experimental group were significantly lower than in the control group (p < 0.05). α-amylase showed a fluctuating trend of decreasing and then increasing, and its activity trend was pyloric ceca > foregut > stomach. The lipase activity of gastric tissues decreased at the beginning and then increased, reaching a minimum at 24 h (2.74 ± 1.99 U·g protein-1). The change of lipase in the pyloric ceca and foregut was increasing and then decreasing. The lipase activity trend was pyloric ceca > foregut > stomach. The chymotrypsin showed a decreasing and increasing trend and then stabilized at 48 h with a pattern of pyloric ceca > foregut > stomach. Similarly, the gut villi morphology was not significantly altered in the acutely salinity-stressed compared to the non-salinity-stressed. This study suggests that salinity may change the digestive function of juvenile yellowfin tuna, thereby affecting fish feeding, growth, and development. On the contrary, yellowfin tuna is highly adapted to 29‱ salinity. However, excessive stress may negatively affect digestive enzyme activity and reduce fish digestibility. This study may provide a scientific basis for a coastal aquaculture water environment for yellowfin tuna farming, which may guide the development and cultivation of aquaculture.