Radio frequency (RF) energy has been successfully applied to rice drying, sterilization, and controlling pests. However, the effects of RF treatment on the microstructure, physicochemical properties, and digestibility of rice have rarely been studied. This study investigated the alteration of a multiscale structure, pasting, rheology, and digestibility of rice grains after the RF treatment. A microstructure analysis demonstrated that the RF treatment caused starch gelatinization and protein denaturation in rice grains with an increasing treatment time. After the RF treatment, indica and japonica rice (IR and JR) remained as A-type crystals, with the formation of an amylose–lipid complex. In contrast, the crystalline structure of waxy rice (WR) was disrupted. The RF treatment led to a decrease in crystallinity and short-range ordered structures. However, the DSC results indicated that the RF treatment enhanced the T_o, T_p, and T_c of IR and JR. The RF treatment resulted in an increase in the resistant starch (RS) of IR and JR, thereby reducing the digestibility. In addition, the pasting profiles of IR and JR after RF treatment were reduced with the increase in treatment time, while the RF-treated WR showed an opposite trend. The storage modulus (G′) and loss modulus (G″) of all samples after the RF treatment obviously increased compared to the control.