Focusing on discovery and cloning of important functional genes, we summarized a set of bioinformatics methods to efficiently dig for profound RNA-seq information. The results showed that 8L:16D, 12L:12D and 16L:8D had 5 807 622, 6 147 140 and 6 116 872 Clean reads, respectively. Comparison between the sequencing data from 8L:16D, 12L:12D, and 16L:8D revealed 200 differentially expressed genes(DEG). The DEG GO functions in the transcriptome library were broadly divided into biological process, cellular component and molecular function categories of 42 branches. Data in the transcriptome could be divided into 22 classes taking the KEGG database as a reference, according to the metabolic pathway, including glycocysis/gluconeogenesis, phototransduction, calcium signaling pathway, and vascular smooth muscle. This study not only conveyed more useful information of CNSS function in flounder, but also provided multi-level information of phototransduction in teleost.