Purple rice flour was modified using heat−moisture treatment (HMT) in three cycles using an oven (OHMT) and autoclave (AHMT) at temperatures of 100 °C and 120 °C, and with moisture levels of 20%, 25%, and 30%. X-ray diffraction was used to analyze the changes in the molecular structure. The swelling capacity, solubility, and starch digestibility, including rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS), were studied in both native and modified purple rice flour. the bioactive compounds and antioxidant activities were also evaluated. Both OHMT and AHMT resulted in a decrease in swelling capacity, solubility, and RDS, but an increase in RS and SDS values compared to the native purple rice flour. All samples showed an increase in relative crystallinity. Both treatments also had an impact on the bioactive compounds and antioxidant activities, leading to a decrease in total phenolic content, total anthocyanin content, and the scavenging activity of DPPH and ABTS radicals compared to the native purple rice flour. The findings suggest that HMT can both improve the functional properties of purple rice flour and hold potential for use in various food industries.