Dysregulation of the biological clock system is recognized as one of the causes of physiological and metabolic disorders and other undesirable disease development in organisms, and the composition of dietary nutrients influences the rhythmic expression of the biological clock system. Ridgetail white prawn (Exopalaemon carinicauda) is an important aquaculture species in the coastal areas of China. However, there is no specialized aquaculture feed for this shrimp, and the effects and mechanisms of environmental regulation of its biological clock system are also not apparent. This study analyzed the changes in the relative expression and expression rhythms of four key biological clock genes under different protein levels by fluorescence quantitative PCR to explore the effects of different protein levels in feeds on the biological clock system of E. carinicauda, and to find a suitable feed protein level for it. The effects of protein level on the synchronization of the biological clock system were also evaluated. Meanwhile, the growth performance and muscle composition were validated and analyzed to ensure the accuracy of this study. The results showed that the expression rhythms of biological clock genes were changed significantly with the increasing feed protein levels in the liver, but not in the eye-stalk, with substantial dysregulation and synchronization deviation between the two biological clock systems. The highest synchronization between the rhythms of expression of the clock genes in the eye-stalk and liver was observed when the feed protein level was 39%, which corresponded to the highest growth performance and optimal muscle protein content (145.83%±4.34%, 18.88%±0.62%). When the protein levels were below or above 39%, the synchronization of the biological clock system was diminished, and the growth performance and muscle registration were also poorly performed. The present study showed that either too high or too low protein levels were detrimental to the maintenance of synchronization of the biological clock system in E. carinicauda and that dietary protein levels around 39% were most suitable for growth and nutrient retention. This study is an innovative approach to "forcefully" alter the rhythm of the peripheral biological clock by altering the protein level in the feed of the shrimp and aligning it with the central biological clock system to maximize growth and metabolic gains, reduce the incidence of metabolic disorders and other diseases, which is important for promoting the practical production and filling the gaps in biological clock research of the E. carinicauda.