Aeromonas veronii has a serious impact on the aquaculture industry and human public health. The type VI secretory system (T6SS) is the virulence regulation system of gram-negative bacteria, of which hcp is the core component. In this study, we constructed the mutant (Δ hcp1) and complemented (C-hcp1) strains of A. veronii TH0426 were using homologous recombination to study the effect of hcp1 gene on the virulence of TH0426. We found that deletion of the hcp1 gene caused fracture of the flagella of TH0426 and significantly affected basic biological characteristics, including motility, biofilm formation, bacterial competition, and flagellate-related gene expression., In terms of pathogenicity, compared with wild-type strain, LD50 of Δ hcp1 decreased 17.5-fold (P < 0.001), adhesion and invasion of EPC ability of the Δ hcp1 significantly decreased 1.5-fold (P < 0.001), and both the bacterial load at 12 h and 24 h and the cytotoxicity of Δ hcp1 decreased significantly. In conclusion, the hcp1 gene can affect the basic biological characteristics and animal pathogenicity of TH0426 cells by regulating flagella assembly. This study is helpful to explaining the gene function of hcp1 in the T6SS and its mechanism of action in animal pathogenesis. •hcp1 gene affects the motility, biofilm formation ability and bacterial competition of A. veronii TH0426.•hcp1 gene is involved in regulating the formation of flagella in A. veronii TH0426.•hcp1 gene negatively regulates flagellar component-related genes in A. veronii TH0426.•hcp1 gene can regulate the virulence of A. veronii TH0426.