BACKGROUNDStarch nanocrystals have received considerable attention, due to their biodegradability, nontoxicity and renewable and abundant sources. The objective of this research is to compare the morphology, physicochemical characteristics and rheological properties of native (NSNC) and waxy rice starch nanocrystals (WSNC).RESULTSBoth NSNC and WSNC exhibited a platelet‐like shape, and they tended to show square‐like platelet morphology with increasing initial amylopectin content. Compared to native starches, three weight loss stages of NSNC and WSNC in thermogravimetric analysis curves were observed, while the thermal depolymerization of NSNC started earlier than that of WSNC. The relative crystallinity of NSNC and WSNC was 38.6% and 48.3%, respectively, which were markedly higher than that of native starches. Fourier transform infrared spectra revealed that NSNC presented the highest ratio of 1045/1014 cm−1 bands among the tested samples, which was probably due to the re‐association of retrograded amylose to double‐helices structure in NSNC. Moreover, the introduction of sulfur atoms on the surface of NSNC and WSNC was confirmed from the results of X‐ray photoelectron spectroscopy. At 5% (w/v) and 10% (w/v) concentration levels, all SNC suspensions exhibited a shear‐thinning behavior as the shear rate increased from 0.1 to 100 s−1.CONCLUSIONSStarch nanocrystals obtained from native and waxy rice starch can be potentially used as reinforcement in biodegradable nanocomposites for packaging, fat replacers, thickening agents and emulsion stabilizers. © 2020 Society of Chemical Industry