Of starch biosynthesis-related enzymes, starch synthases (SSs) and starch branching enzymes (BEs) play important roles in the control of starch structure. Measurements of the particle size distribution, swelling power, differential scanning calorimetry (DSC), X-ray diffraction (XRD) and dynamic viscoelastic measurements were used to investigate the physicochemical properties of rice endosperm starch from SSIIIa, granule-bound starch synthase (GBSSI) and/or BEIIb deficient mutants including double mutants having widespread variation of amylose content and amylopectin structure. The predicted relative starch crystallinity (RSC) of A-type starches and B-type starches of these mutants, as computed based on amylopectin contents, were almost equal. These results suggest that SSIIIa and BEIIb deficiency does not affect the degree of crystallinity of amylopectin. A newly developed double mutant line (ss3a/be2b) with high amylose content (ca. 45%) and a lower proportion of amylopectin short chains showed a higher temperature of gelatinization. Moreover, retrogradation of the gel was extremely rapid. Additionally, be2b with extremely low proportion of amylopectin short chains and lower amylose contents (28%) showed higher gelatinization temperature and more rapid retrogradation than ss3a, with a lower proportion of amylopectin long chains with DP ≤ 33 and higher amylose content (30%). Granules of ss3a/be2b and be2b in gels after viscoelastic measurement were mostly maintained, indicating that most starch granules were not ruptured during heating. These results clarify that not only amylose contents but also the fine structure in amylopectin strongly affected rice gel viscoelastic properties.