Abstract: Biological rhythms play a critical role in the metabolism of organisms. In this study, the juvenile Hippocampus kuda was used as the research object. Four treatments were established, including two photoperiods (L (light)﹕D (dark) 16﹕8, 12﹕12) and two feeding times (2h after light-on the and 2h before light-off), to analyze the interaction between the two biological clock systems of H. kuda and their relationship with nutrient metabolism. The aim was to determine the optimal environmental conditions for artificial breeding and the conditions necessary for the synthesis of important metabolites in H. kuda. Results showed that under long photoperiod (L﹕D16﹕8) with feeding 2h after light-on, H. kuda exhibited the highest specific growth rate in body length (SGR_L) and body weight (SGR_W), as well as the highest condition factor (CF) in all four treatments. Rhythmic expressions were observed in six clock genes (Clock, Bmal1, Per1, Per2, Per3, and Cry1) and eight lipid-related metabolic genes (Hmgcr, Mvk, Mvd, Lss, Fdps, Cetp, Scap, and Srebp1). The trend of clock gene expression in the brain throughout the day, and its peak expression, was consistent with those in liver, which correlated with SGR_L, SGR_W, and CF. However, in the treatments where feeding occurred 2h before light-off, these parameters were significantly lower than those with feeding 2h after light-on. Additionally, the central clock system and the trend of clock gene expression in the brain throughout the day, including peak expression times, differed completely from those in the liver. Only four lipid-related metabolic genes (Hmgcr, Mvk, Scap, and Srebp1) exhibited rhythmic expression under the long photoperiod, while five lipid-related metabolic genes (Hmgcr, Mvk, Mvd, Scap, and Srebp1) exhibited rhythmic expressions under the short photoperiod. The study suggests that H. kuda possesses a comprehensive biological clock system closely linked to lipid metabolism. Combined analysis indicated that stable rhythmic expression of clock genes and metabolic genes could be maintained under the conditions of L:D=16:8 with feeding 2hours after light-on. Under these conditions, the clock gene expression in the brain and liver tended to synchronize, promoting the growth of H. kuda and maintaining the normal lipid metabolism pathway. These findings provide a scientific basis for promoting lipid synthesis and accumulation in H. kuda.