Abstract: Mandarin fish（Siniperca chuatsi） is a famous freshwater fish in China. It has been fed with live baits from fingerlings to adult-fish stage for the past several decades. Development of compound feed instead of live bait counts for the green and healthy development of mandarin fish culture. In recent years, we have found significant differences in growth rates of individuals in our trials with compound feeds for mandarin fish. To explore the differential growth mechanism related with gene expression and regulation, RNA-Seq technology was performed to analyze the transcriptome sequence and differentially expressed genes（DEGs） in four tissues（liver, muscle, brain and stomach） of the fast-and slow-growing groups of S. chuatsi fed with artificial feeds throughout a whole culture period. Compared with the slow-growing group, 920 and 696 up-regulated genes（68.81% and 74.68%） and 417 and 236 down-regulated genes（31.19% and 25.32%） were screened in muscle and brain, respectively, and 347 and 191 up-regulated genes（47.28% and 46.25%） and 387 and 222 down-regulated genes（52.72% and 53.75%）in liver and stomach, respectively, in the fast-growing group. Several DEGs related to growth and metabolism were identified, including glutamate decarboxylase（gadl）, growth differentiation factor（gdf）, lipoprotein lipase（lpl）, fatty acid-binding protein（fabp）. GO functional annotation reveals that DEGs were annotated in biological processes, such as immunity, metabolism, signaling induction, and molecular functions, such as enzyme activity, and signaling receptor binding. KEGG functional annotation showed that DEGs in liver, muscle, brain and stomach were enriched in 17, 15, 12 and 7 pathways respectively, including the pathways related to energy metabolism, lipid metabolism, cell growth and differentiation, neural ligand-receptor interactions, hormone synthesis, signaling induction, such as taurine and taurine metabolism, amino acid synthesis, PPAR signaling pathway, etc. The research results indicated that the growth differentiation in S. chuatsi was co-regulated by multiple genes and a number of potential regulatory networks constituted by these genes. Our works provided insight into the molecular mechanisms that influence the utilization of complementary feedstuff and hence the growth of S. chuatsi.