Changes in physicochemical properties and in vitro digestibility of native whole tartary buckwheat flour (N-T) were studied after heat-moisture treatment (HM-T), heat-moisture-enzyme treatment (HM-E-T), heat-moisture-microwave treatment (HM-M-T), or heat-moisture-citric acid treatment (HM-C-T). The results showed that the contents of total dietary fiber and amylose in whole tartary buckwheat flour increased significantly after treatment (P>12122asd0.05), among which HM-E-T was the most effective, and seconded by HM-C-T. Differential scanning calorimetry analysis indicated that the viscosity of tartary buckwheat powder decreased significantly and the phase transition peak disappeared after treatment. The results of X-ray diffraction showed that the starch after HM-T was still type A, and which was converted to A+B+V polymorph starch after HM-E-T. While the starch after HM-M-T and HM-C-T lost the original crystal structure, and the relative crystallinity of starch decreased from 23.0 (N-T) to 20.9 (HM-T), 18.4 (HM-E-T), 12.6 (HM-M-T) and 10.6 (HM-C-T), respectively. Images from scanning electron microscopy and laser confocal electron microscopy displayed that the microstructure of the whole tartary buckwheat flour changed in varying degrees, and the protein and starch were compounded in a certain extent. In vitro digestion assay showed that the content of resistant starch in whole tartary buckwheat flour increased from 9.69 (N-T) to 11.49 (HM-T), 14.12 (HM-E-T), 11.97 (HM-M-T), 13.01 (HM-C-T), respectively. And the estimated glycemic index (eGI) decreased in varying degrees:57.85 (N-T)>56.03 (HM-T)>55.65 (HM-M-T)>55.18 (HM-C-T)>50.22 (HM-E-T). In particular, HM-E-T had the greatest effect on reducing the eGI value of whole tartary buckwheat flour. Therefore, the combined heat-moisture treatment might more effectively reduce the postprandial grain blood glucose generation index (GI) than HM-T, and the whole tartary buckwheat flour after HM-E-T could be used as an ideal raw material for low GI food.