Boron is an essential micronutrient for plant growth. The BOR gene encodes an efflux-type B transporter, and the grain number of BOR1 mutants decreased. To determine the relationship between TaBOR1 and grain number in common wheat, polymorphic sites within genomic and promoter sequences and haplotypes of TaBOR1.2 were identified. Association analysis was carried out between haplotypes and grain number in a natural population. The results indicated that the exon–intron structures of TaBOR1.1, TaBOR1.2 and TaBOR1.3 were conserved, with sequence homologies ranging from 96 to 97%. Two polymorphic sites were identified, one at − 1085 bp upstream from the start codon of TaBOR1.2 and another at 1102 bp downstream, in ten modern varieties and ten landraces. Two cleaved amplified polymorphic sequence markers were developed, and four haplotypes in 348 modern varieties were detected. Hap-G-A was the favored haplotype and increased grain numbers by 5.22, 3.47, and 4.91 in 2002, 2005, and 2010, respectively. This haplotype has been selected during Chinese wheat improvement; its frequency has increased from 16.21% in the 1960s to 26% in the 2020s. Overall, cleaved amplified polymorphic sequence markers of TaBOR1.2 could be used for marker-assisted selection for increasing the grain number of common wheat.