Display omitted •Starch nanocrystals (SNC) production contained rapid and slow hydrolysis stage.•SNC size reached to nanoscale at hydrolysis of 2 days.•Slow hydrolysis stage mainly involved release and modification of SNC.•Differential centrifugation showed good separation on SNC hydrolyzed for 5 days. Starch nanocrystals (SNCs) were prepared from waxy rice starch via sulfuric acid hydrolysis. The objective focused on the following: i) the hydrolysis kinetics and structural properties of SNCs; ii) the effects of differential centrifugation on the yield and size distribution of SNCs. The hydrolysis was divided into a rapid hydrolysis stage in the initial two days and a slow hydrolysis stage after two days. During the two-day hydrolysis, the average diameter of SNCs reached 244 nm. After two days of hydrolysis, the degree of crystallinity, crystallite size, and melting temperature and enthalpy increased. The proportion of A-branched chains decreased, whereas the proportion of B1-branched chains and molecular weight did not change considerably. Thus, the reaction in the slow hydrolysis stage could be considered as the surface modification and gradual release of SNCs. Furthermore, SNCs with a small size and high charge density could be used for differential centrifugation.