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Amylose largely determines rice grain quality profiles. The process of rice amylose biosynthesis is mainly driven by the waxy (<i>Wx</i>) gene, which also affects the diversity of amylose content. The present study assessed the grain quality profiles, starch fine structure, and crystallinity characteristics of the near-isogenic lines Q11(<i>Wx^lv</i>), NIL(<i>Wx^a</i>), and NIL(<i>Wx^b</i>) in the <i>indica</i> rice Q11 background containing different <i>Wx</i> alleles. Q11(<i>Wx^lv</i>) rice contained a relatively higher amylose level but very soft gel consistency and low starch viscosity, compared with rice lines carrying <i>Wx^a</i> and <i>Wx^b</i>. In addition, starch fine structure analysis revealed a remarkable decrease in the relative area ratio of the short amylopectin fraction but an increased amylose fraction in Q11(<i>Wx^lv</i>) rice. Chain length distribution analysis showed that Q11(<i>Wx^lv</i>) rice contained less amylopectin short chains but more intermediate chains, which decreased the crystallinity and lamellar peak intensity, compared with those of NIL(<i>Wx^a</i>) and NIL(<i>Wx^b</i>) rice. Additionally, the starches in developing grains showed different accumulation profiles among the three rice lines. Moreover, significant differences in starch gelatinization and retrogradation characteristics were observed between near-isogenic lines, which were caused by variation in starch fine structure. These findings revealed the effects of <i>Wx^lv</i> on rice grain quality and the fine structure of starch in <i>indica</i> rice.