Ensuring global food security under climate change and biotic-abiotic stresses requires exploiting the full genetic diversity of crops. Traditional reference genomes capture only a fraction of intraspecific variation, omitting structural variations (SVs) and presence-absence variations (PAVs) that influence key agronomic traits. Pan-genomics, integrating multiple genomes, reveals core and dispensable genes, uncovering novel loci for stress tolerance, yield and quality traits. Advances in de novo assembly, graph-based approaches, and bioinformatic pipelines enable comprehensive pan-genome construction. The super pangenome further incorporates wild and related species, expanding breeding resources. Integrating pan-transcriptomics and pan-epigenomics offers functional insights, establishing pan-genomics as a future reference paradigm for precision crop improvement.