A comparative experiment about the production of starch nanocrystals (SNCs) with/without glucoamylase enzymatic pretreatment by sulfate acid hydrolysis from waxy potato starch (WPS) was employed in the present study. The research focused on the enhancement of the preparation efficiency while improving the dispersion of SNCs at the same time. The enzymatic pretreatment resulted in the decrease of acid hydrolysis duration. The minimum size and best dispersibility of nanocrystals was obtained after 5 days of hydrolysis. X-ray diffraction confirmed the increase of crystallinity (from 33% to 50.8%) and the polymorphic transitions (B-A) for nanocrystals harvested at day 5. The structure of nanocrystals was characterized by FT-IR, which suggested the presence of sulfate ester on the surface of SNCs. Zeta potential and size distribution revealed the prominent stability and dispersibility of nanocrystals at pH 7.0. SEM and TEM revealed that SNCs had square shapes with particle sizes ranging from 50 to 100 nm.