A model of the localized infection with spring viremia of carp virus （SVCV） in zebrafish （Danio rerio） was established to deeply study the mechanisms of viral disease development and the protective functions of microbial communities in fish.The viral load，pathological alterations，and expression profiles of immune-related genes in gill at 1 day，4 days，7 days and 14 days post-infection were analyzed.The changes in the expression profiles of mucosal immune-related genes and surface microbiota in zebrafish gill during the acute infection （4 d） and recovery phase （14 d） were further investigated based on transcriptomic profiling and 16S rRNA sequencing.The results showed that the structure of gill lamellae was disrupted，with respiratory epithelium detachment and inflammatory cell infiltration after infection with SVCV.The expression level of antiviral genes （ifnγ，mxc） and proinflammatory cytokines （tnfα，il1β） was significantly upregulated during the period of acute infection.Concurrent strong inflammatory response and disordered surface microbiota of gill was identified at 4 d，characterized by significantly increased abundance of opportunistic pathogens （e.g.，Pseudomonas spp.） and their translocation into underlying tissues.The body simultaneously initiated immune responses against viral and bacterial infections in the mucous.Both the inflammatory response in gill and the structure of surface microbiota was restored after 14 days of infection.It is indicated that SVCV infection through gills can damage the structure of physical barrier in gill，disrupt the homeostasis of mucosal microbiota，and lead to secondary bacterial infections.Therefore，it is necessary to strengthen the prevention of the outbreaks of bacterial diseases in the case of viral infection.