Starch nanoparticles (SNPs) have unique attributes that make them suitable for specific applications. In this study, we assessed the optimum conditions for the fabrication of SNPs from the rice starches of low- (TCSG2) and medium-amylose rice lines (TK11) using pullulanase debranching combined with annealing treatment and evaluated their physicochemical and digestion properties. The highest crystalline SNP percent recoveries of 15.1 and 11.7% were obtained from TK11 and TCSG2, respectively, under the following debranching conditions: 540-630 NPUN/g, pH 5.0, 60 °C, and 12 h. The percent recovery of the crystalline SNPs by the combined modification of the debranching and the annealing treatment with an extended annealing incubation prepared from TK11 and TCSG2 was significantly increased to 25.7 and 23.8%, respectively. The modified starches from TK11 had better percent recovery of the crystalline SNPs than those from TCSG2. They exhibited a higher weight-average molecular weight (Mw) and a broader/bimodal molecular weight distribution with a higher polydispersity (PDI) (Mw = 92.76-92.69 kDa; PDI = 4.4) than those from TCSG2 (Mw = 7.13-7.15 kDa; PDI = 1.7). Compared to the native counterparts, the color analyses showed that the modified starches from TK11 and TCSG2 exhibited decreased brightness (L*)/whiteness index (WI) values with marked color difference values (∆E) ranging between 6.32 and 9.39 and 10.67 and 11.32, respectively, presumably due to the protein corona formed on the surface of SNPs which induced the browning reaction during the treatments. The pasting properties revealed that the modified starches displayed restricted swelling power with extremely low pasting viscosities, reflecting that they were highly thermally stable. The modified starches, especially those treated with an extended annealing incubation, exhibited marked decreases in the rate and extent of digestion and estimated glycemic index due to the honeycomb-like agglomerates comprising an assembly of densely packed SNPs. The results could provide helpful information for the preparation and characterization of the crystalline SNPs for potential applications such as emulsion stabilizers for Pickering emulsion and health-promoting ingredients.