Heat-moisture treatment (HMT) and annealing (ANN) were applied to modify the proso millet starch, and then the physicochemical properties as well as the in vitro digestion of the modified starch were investigated systematically. Results indicated that HMT and ANN did not change the typical A-type crystallinity. However, both processes cause cracks and dents on the surface of the granule. The gelatinization temperature increased while peak viscosity value, relative crystallinity and gelatinization enthalpy of proso millet starch decreased significantly after HTM and ANN. Meanwhile, a remarkable increase of the slowly digestible starch(SDS) and resistant starch(RS) content was noticed after HTM and ANN modification (the highest content of SDS and RS after HTM and ANN were 9.52 ± 0.82 %, 12.03 ± 1.36 % and 12.15 ± 0.89 %, 8.75 ± 1.63 %, respectively). Those results indicated that the ANN and HMT processes could modify the physicochemical properties and in vitro digestion of proso millet starch efficiently and showed potential application to produce healthy starch food with lower digestion. •Annealing and heat-moisture treatment didn't change the crystallinity type of proso millet starch.•A higher value of To and lower ∆H were observed after annealing and heat-moisture treatment.•No new chemical bonds were generated in proso millet starch during annealing and heat-moisture treatment.•Annealing and heat-moisture treatment decreased the digestion of proso millet starch.