The objective of this study was to investigate granule size and distribution and deformability of granules and their effect on the rheological properties of waxy starch gels. Native (granular) waxy rice gels (10%) were prepared, and their response in oscillatory shear was investigated in the linear and non-linear viscoelastic regime. The results show the gels were mainly composed of aggregated and deformed swollen granules. Significance of granule size and its distribution, deformability of granules, and the molecular characteristics of amylopectin (AP) on storage modulus of those gels was demonstrated. A low degree of deformability of granules, typical for small granules with a broad size distribution and small molecular size of AP with short external chains, resulted in rigid and brittle gels. Highly deformed granules and high AP leachates, however, yielded soft gels. It was found that the transition of elastic to plastic behavior in the non-linear regime (LAOS) was gradual when AP had long external chains, but an abrupt transition was observed with the gel with short exterior chains of AP. Differences in rheological properties of cohesive waxy starch gels appear to be mainly impacted by the varying degrees of granule deformability and rigidity, which is further attributed to a combination of factors, including granule size, particle size distribution, molecular size, the external chain length of amylopectin (AP), and lipid content. The significance of this study is that it will assist the food industry in selecting suitable waxy rice starches to gain desired textural properties of end products.