The bacterial hemorrhagic septicemia caused by Aeromonas veronii is a highly contagious disease leading to high mortality in various aquatic animals, which has become one of the most serious diseases in mandarin fish, Siniperca chuatsi and Siniperca scherzeri. The difference of susceptibility and host immune response between S. chuatsi and S. scherzeri to A. veronii has not been revealed. In this study, the calculated LD50 of A. veronii SJ4 to S. chuatsi and S. scherzeri was 3.8 × 105 CFU/ mL and 4.8 × 106 CFU/mL, respectively, indicating S. chuatsi displays more susceptible to A. veronii than S. scherzeri. The differences of immune response between S. chuatsi and S. scherzeri infected by A. veronii SJ4 was analyzed by transcriptome technology. A total of 6010 and 1676 differentially expressed genes (DEGs) of kidneys were detected in the S. scherzeri experimental group (S-S-E/C) and S. chuatsi experimental group (S-C-E/C) at the 12 hpi, respectively. GO and KEGG functional analysis of DEGs indicated that numerous enriched immune terms were mainly related to antigen processing and presentation, toll-like receptor signaling, and C-type lectin receptor signaling. 8 DEGs (CLE, HSP90, IL6, MHC I, MHC II, RAS, TLR5 and TLR9) were selected from these immune related pathways, and the spatiotemporal expression of these DEGs in S. chuatsi and S. scherzeri were evaluated and compared. The results showed that CLE, HSP90, IL6, MHC I, MHC II, RAS, TLR5 and TLR9 in S. scherzeri after A. veronii infection were significantly up-regulated than in S. chuatsi. Our results indicated that these immune-related genes may exert a pivotal role during the initial phase of infection, and the priming speed of these immune-related genes lead to the differences in host immunity. This study screened the potential genes and pathways which involved in the immune response of mandarin fish, which helps for further understanding on fish immune. By selecting immune-related genes and comparing the immune mechanisms of S. chuatsi and S. scherzeri at the transcriptome level, the research offers new insights for the genetic breeding of Siniperca species to enhance infection resistance.