Ammonia accumulates in the process of shrimp culture and has a strong toxic effect on shrimp survival, physiological metabolism and immune function. Shrimp can adapt to ammonia stress by regulating lipid metabolism. In the present study, to explore the regulatory mechanism of lipid metabolism in ammonia tolerance of Penaeus vannamei (3.08 ± 0.40 g) based on the energy supply, a 96-h ammonia stress experiment was conducted, and energy homeostasis and lipid metabolism responses in the hepatopancreas, muscle and gills of shrimp were observed at total ammonia concentrations of 0 (control group), 6.42, 32.11, and 64.22 mg/L. The cumulative mortality of shrimp increased significantly with increasing ammonia stress concentration. Exposure to ammonia stress significantly decreased the content of adenosine triphosphate (ATP) and the adenylate energy charge (AEC) in the hepatopancreas, muscle and gills, whereas the relative expression of the AMPK, TOR, and SREBP genes was significantly upregulated. The activities of fatty acid synthase (FAS), acetyl-coenzyme A carboxylase (ACC), and carnitine palmitoyltransferase I (CPT-1) and the peroxisome proliferator-activated receptor-α (PPAR-α) level in the hepatopancreas were significantly increased, whereas the opposite was observed in the muscle and gills. In general, the triglyceride (TG) content of the hepatopancreas increased significantly with increasing ammonia concentration. The results indicated that ammonia stress reduced cellular energy levels in the hepatopancreas, muscle and gills of P. vannamei , thereby inducing the activation of the AMPK signaling pathway in these tissues and resulting in increased levels of lipid decomposition and energy supply in the hepatopancreas. However, the activation of the AMPK pathway did not improve the levels of lipid decomposition or energy supply in the shrimp muscle and gills. • Ammonia stress significantly decreased the ATP content and the AECs in shrimp tissues. • Ammonia stress induced significant upregulation of AMPK, TOR, and SREBP in shrimp tissues. • Fatty acid decomposition and synthesis were enhanced in the hepatopancreas in shrimp exposed to ammonia stress. • The imbalance in energy homeostasis caused by ammonia stress may be an important cause of shrimp death.