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Abstract 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. Pan-genome analysis offers a platform to evaluate genetic diversity of a species via investigation of its entire genome repertoire. This review highlights the progress achieved in understanding crop pan-genomics, discusses biological activities that cause structural variation, reviews important agronomical traits affected by structural variation, and presents perspectives on the application of pan-genomics in crop improvement. [ABSTRACT FROM AUTHOR]