Elucidating the genetic basis of starch pasting and gelatinization properties is crucial for enhancing the quality of maize and its utility as feed and industrial raw material. In maize,ZmSBEgenes encode important starch branching enzymes in the starch biosynthesis pathway. In this study, we re-sequenced the genomic sequences ofZmSBEI,ZmSBEIIa,ZmSBEIIb, andZmSBEIIIin three lines called 335 inbred lines, 68 landrace lines, and 32 teosinte lines. Analyses of nucleotide polymorphisms and haplotype diversity revealed differences in the selection patterns ofZmSBEI,ZmSBEIIa,ZmSBEIIb, andZmSBEIIIduring maize domestication and improvement. A marker–trait association analysis of inbred lines detected 22 significant loci, including 18 SNPs and 4 indels significantly associated with three maize starch physicochemical properties. The allele frequencies of two variants (SNP17249C and SNP5055G) were examined in three lines. The frequency of SNP17249C inZmSBEIIbwas highest in teosinte lines, followed by landrace lines, and inbred lines, whereas there were no significant differences in the frequency of SNP5055G inZmSBEIIIamong the three lines. These results suggest thatZmSBEgenes play an important role in the phenotypic variations in the starch physicochemical properties in maize. The genetic variants detected in this study may be used to develop functional markers for improving maize starch quality.