Abstract: Skeletal muscle comprises 30%—80% of fish body weight, which is very important for the health and economic value of fish. Elopichthys bambusa is a high-value economic fish, but the molecular mechanisms underlying muscle development in its juveniles remain unclear. In this study, the muscle development characteristics of juvenile Elopichthys bambusa at different developmental stages and under different domestication strategies were discussed by using histological and transcriptome analysis, complemented by fluorescence quantitative PCR verification. The results showed that the mosaic proliferation of muscle fibers of Elopichthys bambusa larvae began on the 22nd day post-hatching (dph). During the early stage of muscle mosaic proliferation, genes related to MyoGenic regulators (myog and myod), the myostatin gene (mstn), muscle satellite cell marker gene (pax7), and muscle differentiation-related genes (myl3, tnni2, myoz2, tpm1) were actively involved. In addition, the use of artificial compound feed can improve muscle metabolism and promote growth in juvenile Elopichthys bambusa, with the 22 dph group showing higher weaning efficiency and better weaning effect. This study provides a foundation for understanding the characteristics and molecular mechanism of muscle development in Elopichthys bambusa and provide a theoretical reference for large-scale farming practices.