Asynchrony among the various biological clock systems is considered one of the primary reasons for the occurrence and development of adverse diseases such as physiological and metabolic disorders. Changes in feeding frequency can affect the expression rhythms of the biological clock system, thereby affecting biological growth and development. To investigate the effect of feeding frequency on the growth of Exopalaemon carinicauda and determine the appropriate feeding frequency for its cultivation, this study analyzed the rhythmic changes in biological clock gene expression in the eyestalk and liver of E. carinicauda under varying feeding regimens, evaluated the impact of different feeding frequencies on the synchronization of biological clock systems in E. carinicauda, and simultaneously verified growth and muscle composition changes through cultivation. The results showed that when the feeding frequency was less than 3 times per day, the expression rhythm of biological clock genes did not change in response to changes in feeding frequency. Similar expression cycles and peak phases were observed in both the eyestalk and liver, with no significant difference in their respective expression levels. However, when the feeding frequency increased to 4 times per day, there were significant changes in the expression rhythm in the liver, which manifested as changes in the expression cycle, phase shifts, and expression levels themselves. Notably, when the feeding frequency is 3 times per day, the synchronization of clock gene expression rhythm between the eyestalk and the liver is at its highest. Furthermore, the results also showed that the growth of E. carinicauda increased with feeding frequency from 1 to 3 times/d. Indeed, the specific growth rate (SGR) and weight gain rate (WGR) were (6.65±0.98)%/d and (199.46±5.42)%, respectively. Concurrently, as the feeding frequency increased, so did the crude protein and crude fat content in the muscle tissue, reaching a maximum in the treatment C with (19.98±0.04)% and (1.88±0.23)%, respectively. In summary, the feeding frequency has a significant impact on the expression rhythm of circadian clock genes in the liver of E. carinicauda, indicating its modulatory effect on resetting or regulating the peripheral circadian clock system.