The Wx gene is the major gene controlling amylose synthesis in rice endosperm. So far, the Wx gene can be mainly classified into five common alleles, wx, Wx t , Wx g1 , Wx g2 , and Wx g3 , according to their amylose phenotypes. Besides, the Wx allelic variation was also found to play an important role in regulating other physicochemical properties of rice starch. However, the specific physiological and starch structural mechanisms are not clear yet. With a set of singlesegment substitution lines harboring five different Wx alleles, the genotype differences in amylopectin structure and dynamic changes of activities of key starch synthesis enzymes were investigated. The distinct Wx genotype difference in chain length distribution of amylopectin was confirmed by size exclusion chromatography. There were clear allelic differences in activities of starch synthesis enzymes during grain filling. The Wx allelic variation had the highest impact on the activities of starch branching enzyme, followed by pullulanase, and soluble starch synthase, while no influence on isoamylase activity. Differences in structural features of amylopectin and mean enzyme activities during grain filling period correlated well with most of the variations in starch property traits. These findings indicate that the Wx allelic variation may affect starch structure and physicochemical properties through selectively influencing activities of starch synthesis enzymes in developing rice grains. The present results will contribute to our understanding of the regulation of starch biosynthesis in rice endosperm.