Feed is very important for fish farming. The appropriate composition and proportion of feed ingredients can promote the growth of fish, maintain normal physiology and behavior, and even improve the resistance ability to disease and stress, etc. The core of artificial compound feed (ACF) is the composition and proportion of lipid, protein, and carbohydrate, which are also the main nutritional components required by fish. Appropriate levels and ratios can promote fish growth and save costs, and the improper would affect the biological clock systems of fish, leading to metabolic abnormalities. This study explored the preparation of ACF for H. kuda. The composition and proportion of the three main nutrients in ACF were screened based on the synchronicity between six pairs of clock genes (Clock, Bmal1, Per1, Per2, Per3, Cry1, and Cry2) in the central and peripheral clock systems, as well as the expression of eight lipid-metabolism genes (Hmgcr, Mvk, Mvd, Lss, Fdps, Cetp, Scap, Srebp1, Srebp2) in the liver and their synergy with liver clock genes. The results showed that, based on several parameters such as gene expression cycle, relative expression level, and top phase appearance time, the best synergy between the central and peripheral circadian clock systems was observed in ACF with crude fat content of 8.80%, crude protein content more than 38.4%, and carbohydrate content of 23.5%. Based on the expression relationship between lipid metabolism genes and circadian clock genes in the liver, it was further clarified that the optimal levels of fat, protein, and carbohydrate were determined with 8.80%, 38.4%, and 23.5%, respectively. After 4 weeks of breeding validation, compared with frozen Mysis, the screened ACF fed for H. kuda showed significant advantages in body length specific growth rate (SGR), body weight specific growth rate (SGR), and feed conversion rate (FCR).