Micropterus salmoides is a species of carnivorous teleost. Annually, a large amount of forage fish were used as food for M. salmoides. The residual forage fish not only increase the culture costs, but also pollute environment seriously. In order to protect the environment and cut down culture costs, it is necessary to breed the strain which can digest and absorb formulated feed efficiently to reduce the utilization of forage fish. In this study, for promoting selective breeding of the M. salmoides strain suitable for formulated feeds, bait domestication was carried out in juvenile M. salmoides of breeding group and non-breeding guoup. On the 14th day and the 16th day after bait domestication, the growth traits including body weight, total length and body height were measured. At the same time, seven candidate Unigenes related to energy metabolism with SNPs were selected from the transcriptome of M. salmoides. The SNP sites were genotyped by using of SNaPshot in a bulked segregate analysis (BSA) population with 129 minimax individuals, and the association analysis between genotypes and growth traits were detected. After analysis by using of SPSS 19.0 software, the results showed that, among the seven SNP sites, C1332G in Unigene031044, A741G in Unigene085384, A284G in Unigene022319, were significantly associated with body weight, full length and body height. By BLAST analysis, Unigene031044, Unigene085384 and Unigene022319 were predicted as hydroxysteroid 17-beta dehydrogenase 12-B (hsd17b12b), Acyl-CoA synthetase long-chain family member 1 (acsl1) and Succinate dehydrogenase complex assembly factor 2 (sdhaf2). The results indicated that the SNP sites in above three genes probably play the roles of regulating lipid metabolism and three carboxylic acid cycle, and help M. salmoides to improve the capacity to digest, absorb and utilize formulated feed. The current three SNPs can be used as candidate markers for breeding M. salmoides suitable for formulated feeds.