A two‐factorial experiment (temperature with three levels: 23°C, 25.5°C and 28°C; diet with four kinds: live Artemia sp., copepods, live Artemia sp. + copepods and frozen Neomysis awatschensis [FNA]) was carried out to evaluate the effects of different temperatures and diets on biochemistry in the juvenile lined seahorse (Hippocampus erectus) for thirty days. The juveniles (n = 1260, body height: 5.1 ± 0.48 cm, initial wet weight: 0.42 ± 0.14 g) were distributed in 36 experimental aquaria (35 individuals each). Each treatment had 3 replicates. On day 30, the seahorses were vacuum freeze‐dried at −56°C before chemical analysis. Amino acids, fatty acids, Se, Zn, nucleosides, and nucleotides were measured in the present study. The results show that temperature, diet, and their interaction significantly affected all components. The content of amino acids and fatty acids in the juveniles fed FNA at 23°C was the highest. The content of Zn in the juveniles fed FNA at 23°C, and the content of Se fed Artemia sp. + copepod at 25.5°C were the highest, respectively. The content of uracil, adenine, and thymidine in the juveniles at 23°C was significantly lower than those treatments at 25.5°C and 28°C. The levels of uracil, guanine, cytosine, uridine, and guanosine at 28°C were significantly higher than those at 23°C or 25.5°C when fed Artemia sp. + copepod. The juveniles fed Artemia sp. + copepod and Artemia sp. at 28°C has the highest comprehensive scores of nucleoside and nucleotide. In conclusion, FNA is the best feed to improve the content of amino acids, fatty acids, and Zn at 23°C.