Food and water environments are key factors affecting juvenile survival rate in seahorse aquaculture. In order to adjust to local conditions, different seahorse (Hippocampus erectus) breeding models were developed in North and South China. Seahorses in North China were commonly fed Artemia in indoor containers with a stable water environment, while most seahorses in South China were fed copepods in outdoor concrete ponds. Firstly, we compared the effect of food type on juvenile seahorses based on a one-month feeding experiment and found no significant difference in body length. However, the insulin-like growth factor 1 (IGF-1) gene expression was significantly higher in the liver of seahorses fed copepods than in the lever of seahorses fed Artemia, suggesting that copepods promoted better growth. A high expression of stress-related genes, namely, heat shock proteins 70 (HSP70) and Mn superoxide dismutase (Mn-SOD), in the liver of the seahorses that were fed copepods suggested that copepods might cause more stress on juveniles. Lower leptin gene expression in the liver of seahorses fed Artemia than in those fed copepods proved that Artemia was better for satiating the juveniles. Furthermore, the potential effects of salinity (15 and 30 ppt) and ammonia‑nitrogen (0, 5, and 15 mg/L) on juvenile seahorse physiological stress were studied through a 5-d orthogonal experiment. Both lower salinity and higher ammonia‑nitrogen increased the ventilation rate significantly. Low salinity caused a rapid increase in the ventilation rate on day 1, while high ammonia‑nitrogen was the main factor during the later period (days 2–5). Significant changes in the mRNA expression of genes, including Na+: K+:2Cl− cotransporter 1 (NKCC1) and Na, K-ATPase (NKA) in the gill, HSP70, Mn-SOD, glutamate dehydrogenase (GDH), and glutamyl synthase (GS) in the liver, indicated that seahorses are sensitive to acute salinity decline. In addition, high ammonia‑nitrogen exposure significantly changed the expression of genes (i.e., Mn-SOD, GDH, and GS) in seahorses exposed to low salinity level, while no significant variation was observed in seahorses exposed to normal salinity, suggesting that salinity decline might increase the negative effects of ammonia‑nitrogen stress. The present study provides a better understanding of how food, salinity, and ammonia‑nitrogen affect juvenile seahorses, and will be potentially important to improve animal welfare and increase production efficiency.