Abstract: Tripartite motif (TRIM) proteins is a structurally conserved protein group that plays an important role in many biological processes, such as apoptosis, cycle regulation, cellular responses to viruses and inflammatory response. Trim47 is a member of the TRIM family. In this study, the CRISPR/Cas9 technique was employed to knockout trim47 of zebrafish. Brain and spleen of TRIM47^–/–(trim47 knockout) and WT (wildtype) zebrafish were collected for RNA-seq analysis to identify differentially expressed genes (DEGs). A total of 271 DEGs were identified. After a brief analysis, these DEGs were annotated into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and three ontologies following gene ontology (GO) enrichment analysis. DEGs were more concentrated in cell adhesion and glutamatergic synapse signaling pathway in brain of TRIM47^–/– group as compared with WT group. In spleen, DEGs of TRIM47^–/– group changed in complement and coagulation cascades signaling pathway as compared with WT group. The complement pathway-associated genes in brain and spleen were verified using qRT-PCR, which were consistent with the transcriptome data. These results indicated that Trim47 played an important biological role in spleen and brain, particularly involved in innate immune function through complement pathway. In vivo infection experiments showed that trim47 knockout increased the infection rate of Spring Viremia of Carp Virus (SVCV) in zebrafish. In conclusion, these findings provided new insight into the function of the TRIM members in innate immunity.