In order to explore the molecular basis of the higher growth rate in FFRC No.2 strain common carp(Cyprinus carpio), we utilized comparative transcriptomics analysis using next-generation sequencing and examined transcript profiles of the muscles from high-growth (HG) (average final body weight FBW= 522.3 g, SE=11.03) and slow-growth (SG) (average FBW= 314.9 g, SE=7.16) individuals. Two poly (A)⁺ RNA-seq libraries were constructed and sequenced using paired-end (PE 2×125) Illumina technique. All sequence data were submitted to NCBI SRA database (SRP078896). A total of 286 118 576 reads were generated, resulting in 392 238 assembled contigs, corresponding to 348 144 unique genes and their length ranged from 200 to 32 499 bp. We firstly performed a functional annotation on the assembly using first aligning by BLASTx with cut-off e-value < 1×10^–10, then all assembled contigs were blasted against the Nr database, UniProt-SwissProt database, KEGG database and COG database, respectively. The contigs hit 56.01%-77.71% of the unique proteins of Danio rerio, Fugu ocellatus, Oryzias latipes, Gasterosteusaculeatus, C. carpio and Oreochromis niloticus. And 93 462 contigs containing 129 047 simple sequence repeats (SSRs) were identified. For the assembled contigs which had hits against with Nr database, 112 001 annotated contigs were found to contain the Open Reading Frame (ORF). The ORF length ranged from 27 to 32 490 bp with an average of 554.68 bp. To reveal the underline mechanism of the muscle growth rate in FFRC No. 2 strain C. carpio, we performed a differential expression analysis between the two muscle transcriptomes. Based on the criteria of |log₂FC| ≥ 1 and FDR ≤ 0.05, we identified 749 differentially expressed genes in HG fishes compared with SG fishes, of which 348 genes were up-regulated and 401 genes were down-regulated genes in HG fishes. Several key genes related to muscle growth, i.e. mb,myl2b, tnni1,fhl1, lamb3,pdk2 and igfbp7 were identified. All these DEGs were subjected to GO term enrichment and KEGG pathway analysis to obtain the potential function annotation. These DEGs were enriched in different gene ontologies and pathways. The KEGG pathway analysis results showed that the cardiac muscle contraction pathway and hypertrophic cardiomyopathy (HCM) pathway were found significantly enriched of DEGs, in which tnni1, tnni2,mybpc1, actn2 and tpm2 serve as key regulatory proteins. These findings will facilitate gene function study and help to understand the molecular mechanisms of muscle growth in C. carpio by breeding and improve the molecular selection method of the specific strain with fast growth.