To explore the mechanism of the effects of different sub-types of starch branching enzyme (SBEIIa and SBEIIb) on the structure and physicochemical properties of endosperm starch in rice, the common rice variety 'Jiahua No.1' and mutants of SBEIIa and SBEIIb were used as experimental materials. The results showed that, compared with 'Jiahua No.1', the starch crystals of SBEIIa mutant changed from angular to spherical, the amylose content (AC) did not change significantly, and the resistant starch (RS) content increased by over 2 times. In addition, the SBEIIb mutant also had spherical crystals with smaller shape and stronger adhesion, accompanied by free lipids, however, its AC and RS content increased by over 25.6% and 6 times, respectively. Apart from the difference with 'Jiahua No.1', there existed a significant difference in the degree of gelatinization between the mutants of SBEIIa and SBEIIb. These results suggest that the two isoforms of starch branching enzyme genes have different functions and roles in starch synthesis, which has some guiding significance for breeding high resistant starch rice varieties.