Thermal treatment has been used to modify starch properties, but few studies pay attention to the change in highland barley starch (HBS) under the whole kernel treatment. The different effect of superheated steam (SS) on the HBS properties from other traditional thermal treatment is still unclear, not mention to the exactly structural change of HBS. This study explored the different effects of SS, steam and roasting treatments of HB kernel on the multi-scale structure, rheological and digestive properties of HBS. Thermal treatments led to the aggregation of HBS granules, the rough surface, and the absence of Maltese cross, as well as the increase in short-chain length ratio and amylose content. Compared with steam and roasting treatments, SS treatment increased the average molecular weight of HBS at 140 °C while reduced it at 180 °C due to starch interactions and depolymerization effect. Multi-scale structure analysis revealed that SS-180 showed the most significant disruption of HBS crystalline structure, the disorder of short-range structure, the decrease in double helix content and the disruption of lamellar structure. These structural changes of HBS resulted in the enhanced thermal stability, and decreased values of GâČ and Gâł representing the weaker gel structures. Meanwhile, much more resistant starch was converted from rapid digestible starch and slowly digestible starch in SS-treated HB than other thermal-treated HB. In particularly, the most change in multi-scale structure of HBS caused by SS-180 was responsible for its best thermal stability, weakest gel structures and slowest starch digestive rate.