BnaGVD is a comprehensive genomic variation database for rapeseed (Brassica napus), integrating 34.6 million high-quality SNPs and 12.3 million InDels from 1,007 worldwide accessions across 39 countries. It is built on three reference genomes (Darmor-bzh, Tapidor, and NY7) and provides functional gene annotations from databases such as Nr, GO, KEGG, and Pfam. The platform offers search modules for variations and genes, along with built-in tools for GWAS (BnaGWAS), principal component analysis (BnaPCA), population structure analysis (BnaStructure), and primer design. Users can browse genomic data via GBrowse and download all datasets freely. BnaGVD supports functional genomics, marker-assisted breeding, and population genetics studies in rapeseed.