Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species.There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species.Pan-genome analysis offers a platform to evaluate the genetic diversity of a species via investigation of its entire genome repertoire.Although a recent wave of pan-genomic studies has shed new light on crop diversity and improvement using advanced sequencing technology,the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited.In this review,we highlight the progress achieved in understanding crop pan-genomics,discuss biological activities that cause SVs,review important agronomical traits affected by SVs,and present our perspective on the application of pan-genomics in crop improvement.