To prevent starch nanocrystals (SNCs) that are generated at an early stage from being hydrolyzed excessively, this study proposed a new separation method, named “neutral dispersion and acidic precipitation.” SNCs were prepared from waxy potato starch by sulfuric acid hydrolysis. Based on the results of kinetics and molecular weight, the hydrolysis was divided into three stages, e.g., rapid (initial 1 day), medium (subsequent 1 day) and slow stage (2–5 days). The rapid and medium stages were related to the degradation of amorphous region in starch, and the slow stage mainly referred to SNC release. Therefore, the method was developed to separate SNCs at the slow stage. After centrifugation at 6000 rpm, large particles were removed from the SNC suspension under pH 7. The SNCs with small average size and crystallite size, high relative crystallinity (RC), and high dispersion stability in the supernatant were retained and were then precipitated entirely under pH 5, because pH 5 led to the reduction of dispersion stability of SNCs. Meanwhile, the hydrothermal and dry-thermal stability of separated SNCs were significantly promoted. The separation method has the potential in SNC preparation for increasing the yield and collecting products with small size and high RC. Display omitted •Starch nanocrystals (SNCs) were prepared from waxy potato starch by acid hydrolysis.•The generation of starch nanocrystals mainly occurred in the slow stage.•A method of neutral dispersion and acidic precipitation was used to separate SNCs.•The method avoided excessive hydrolysis of SNCs and reduced the size distribution.•Separated SNCs had high relative crystallinity and thermal stability.