This study aimed to identify differentially expressed genes (DEG), proteins (DEP), phosphoproteins (DEPP) and phosphosites in elovl6−/− zebrafish in comparison to WT and to further investigate the highly enriched pathways so that we can provide a comprehensive and systematic insight into the regulatory networks of elovl6. Meanwhile, our results also provide the potential therapeutic targets for elovl6-involved metabolic diseases risking to human health. This evidence concerns the gene DEPP1 and metabolic disease.