The application provides a gene structure variation combination, primers and application thereof significantly related to a Brassica napus growth period, belongs to the field of plantmolecular breeding and gene editing technology, and the gene structure variation combination comprises one or more of "DEL00146035 gene structure variation + INS00146036 gene structure variation", DEL00006200 gene structure variation, "DEL00018831 gene structure variation + INS00018834 gene structure variation". BnaC6.MED13 As a major genetic locus (initial flowering time, final flowering time), the gene structure variation combination is respectively composed of BnaA2.GA20ox2 , BnaA4.SPL15 A gene structure variation combination of a genetic locus (silique maturation time) can accurately and quickly and accurately identify a short growth period of a rapeseed variety.