In this study, pure-breeding and crossbreeding of Sinocyclocheilus grahami were established to test heterosis and expression of growth-related genes which were examined in the first-generation (F1). Genetic distances results showed that Muyang river (M) and Sanbaimu reservoir (S) populations had smaller interspecific distances (genetic distance: 0.000) while larger distances were shown to other two populations (0.024 of Jiuzhai vauclusian spring [J] and 0.044 of Chenglong vauclusian spring [C]). Full-sib families were created by using the Muyang river population as females: MM, MS, MJ and MC. Growth performance had significant differences between each group of F1 hybrids; the fastest growth group was shown in MJ while the slowest was in MS. For growth-related genes, the fast growth group of MJ hybrids showed significantly higher levels of ghrelin expression in strong expression tissues of the intestine and liver. Among the four combinations, mRNA levels of insulin-like growth factor I (IGF-I) were the highest expression in MJ hybrids than others in all tested tissues. Myostatin b and somatostatin1 (SST1) were strongly expressed in the brain and MJ hybrids showed relatively lower expression level. In the muscle, slow growth group of MS hybrids showed extremely higher expression levels of these two genes, especially SST1 gene. In conclusion, associating growth with growth-related genes expression indicated faster growth of crossbreeding in S. grahami and can make a contribution to commercial fish production in the future.