In recent years, RNA-seq technology has been used in fish researches. The transcriptome analysis in Ctenopharyngodon idella kidney cell lines (CIK) is focused on virus, and that based on bacteria or lipopolysaccharide (LPS) is rarely reported. In order to elucidate the mechanism of mammalian sterile20-like kinase 2 (mst2) in C. idella during immune response, we analyzed and verified the transcriptome sequence of CIK incubated with LPS after being interfered with mst2 by small interfering RNA technology (siRNA). Firstly, a total of 22 374 unigenes were obtained from the original sequence data by De novo assembly, of which 21 199 genes were known and 1 175 new genes were predicted. Secondly, the analysis of unigenes expression showed that there were 38 differential genes (differentially expressed genes, DEGs) including 16 up-regulated genes and 22 down-regulated genes. Thirdly, 38 DEGs were verified by quantitative real-time PCR (qRT-PCR). The results showed that the qRT-PCR analysis was consistent with transcriptome sequencing, indicating that the transcriptome sequencing was reliable. 38 DEGs in CIK cells were mainly involved in immune metabolism pathway, containing MAPK signal pathway, endocytosis pathway, autophagy pathway and cytokine receptor interaction pathway. Moreover, after being interfered with mst2 and treated with LPS, the detection of apoptosis-related genes showed that the transcriptional levels of pro-apoptotic genes (fas, bad1, bad2, caspase-3, caspase-8 and caspase-9) were up-regulated, while the anti-apoptotic genes (bcl2) were down-regulated. Therefore, it was proved that interfering mst2 could induce cell apoptosis after LPS treatment. To sum up, mst2 can participate in the body's immune response by regulating apoptosis-related processes. The present results preliminarily clarified the molecular mechanism of mst2 in grass carp during immune response, and may provide some basic theoretical reference for the prevention and control of grass carp bacterial diseases.