Sago starch has weaknesses such as low thermal stability and high syneresis. Modifications were made to improve the characteristics of native sago starch. In this study, sago starch was modified by autoclave-heating treatment (AHT), osmotic-pressure treatment (OPT), octenyl-succinic anhydride modification (OSA), and citric acid cross-linking (CA). This study aimed to examine the changes in chemical composition, crystallinity, and functional properties of the native sago starch after physical and chemical modifications. The results show that physical modification caused greater granule damage than chemical modification. All modification treatments did not alter the type of crystallinity but decreased the relative crystallinity of native starch. New functional groups were formed in chemically modified starches at a wavelength of 1700–1725 cm−1. The degree of order (DO) and degree of double helix (DD) of the modified starches were also not significantly different from the native sample, except for AHT and OPT, respectively. Physical modification decreased the swelling volume, while chemical modification increased its value and is inversely proportional to solubility. AHT and OPT starches have the best freeze–thaw stability among others, indicating that both starches have the potential to be applied in frozen food.