As one of the structural tissues of fish skeletal muscles, slow muscle plays an important role in physiological and metabolic activities. The Hedgehog (Hh) signaling pathway has been reported to be involved in regulating the development and metabolism of slow muscle in fish. The underlying molecular mechanisms by which the Hedgehog (Hh) signaling pathway governs metabolic homeostasis within the slow muscle tissue of fish remain an enigma. In order to reveal the functional regulatory role of the Hh signaling pathway in the slow muscle of Chinese perch ( Siniperca chuatsi ), Cyclopamine was used to inhibit the Hh signaling pathway and Illumina sequencing technology was employed to explore the effect of inhibiting the Hh signaling pathway on slow muscle transcriptomes. In this study, a total of 666 differentially expressed genes (DEGs) were obtained between the control and Cyclopamine-treated groups. Functional enrichment analyses showed that the DEGs are mainly enriched in signaling pathways related to autophagy and metabolism, such as the mTOR signaling pathway, the autophagy pathway and the FoxO signaling pathway. The Western blotting analysis showed that the autophagy levels increased after treatment with Cyclopamine. Transmission electron microscopy results showed that the number of autophagic lysosomes was reduced in the Cyclopamine-treated group. The above results suggest that the Hh signaling pathway may play a key role in the regulation of autophagy and metabolism in slow muscle of Chinese perch, thus ensuring normal physiological activities in their muscles. In addition, the present study provides a direction for further elucidating the role of Hh signaling pathway in regulating the dynamic balance of metabolism in the slow muscle of Chinese perch.