This study modified native highland barley (HB) flour by heat–moisture treatment (HMT) at different temperatures (90, 110, and 130 °C) and moisture contents (15%, 25%, and 35%). The effects of the treatment on the pasting, thermal, rheological, structural, and morphological properties of the native and HMT HB flour were evaluated. The results showed that HMT at 90 °C and 25% moisture content induced the highest pasting viscosity (3626–5147 cPa) and final viscosity (3734–5384 cPa). In all conditions HMT increased gelatinization temperature (To, 55.77–73.72 °C; Tp, 60.47–80.69 °C; Tc, 66.16–91.71 °C) but decreased gelatinization enthalpy (6.41–0.43 J/g) in the HMT HB flour compared with that in the native HB flour. The HB flour treated at 15% moisture content had a higher storage modulus and loss modulus than native HB flour, indicating that HMT (moisture content, 15%, 25%, and 35%) favored the strengthening of the HB flour gels. X-ray diffraction and Fourier-transform infrared spectroscopy results showed that HMT HB flour retained the characteristics of an A-type crystal structure with an increased orderly structure of starch, while the relative crystallinity could be increased from 28.52% to 41.32%. The aggregation of starch granules and the denaturation of proteins were observed after HMT, with additional breakage of the starch granule surface as the moisture content increased. HMT could increase the resistant starch content from 24.77% to 33.40%, but it also led to an increase in the rapidly digestible starch content to 85.30% with the increase in moisture content and heating temperature. These results might promote the application of HMT technology in modifying HB flour.