In this study, lily starch was modified by high‐pressure homogenization (HPH), O3, or their combinations and the effects on physicochemical and functional properties, as well as in vitro digestibility were investigated. The results showed that HPH did not significantly affect lily starch properties (p > .05), while O3 effectively modified the starch whether it was used separately or combined with HPH. The oxidation damaged the starch surface, increased particle size, and decreased the relative crystallinity, whereas the crystalline structure was still B‐type. The pasting and thermal properties of O3‐HPH‐treated samples were significantly improved, and their solubility and swelling power were significantly higher than those of the native starch (p < .05), especially at 90 °C. Besides, O3‐HPH caused the lowest resistance starch compared with other treatments, which were 63.79% and 35.30% in uncooked and cooked samples. Therefore, O3‐HPH combination treatment could be a potential method for effectively modifying lily starch. Practical applications The poor characteristics limited the native lily starch application in the industry. Hence, there is an urgent need to modify the lily starch and improve its properties. This paper presented the potential of combination of HPH and O3 (HPH‐O3 and O3‐HPH) for modifying lily starch. Compared with HPH or O3 alone, combination treatment induced a better pasting and thermal properties of the starch, as well as higher solubility and swelling power at the high temperature, especially for O3‐HPH. In addition, the combination treatments decreased the content of resistance starch and improved the digestibility of lily starch. Therefore, combination of HPH and O3 conferred better functionality on the starch than single treatment, which could broaden the application of lily starch in the industry.