The effects of heat-moisture treatment (HMT) and annealing (ANN) modification with plasma-activated water (PAW) (HMT and ANN are collectively referred to as HM) on the physicochemical, structure, functional, and digestive properties of native corn flour (NCF) were investigated. X-ray diffraction analysis revealed a decrease in the relative crystallinity of HMT corn flour compared to ANN and native flour, without crystalline type transformation. The short-range order of HM groups was decreased (the double helices were disrupted), and the protein secondary structure, particularly the relative content of parallel beta-sheet and random coil, was found to be altered according to Raman and Fourier transform infrared spectroscopy measurements. HM treatment increased the gelatinization temperatures and solubility of NCF, with decreased swelling power. HM-PAW resulted in a larger particle size distribution. The microstructure showed that HM treatment causes partial melting of the starch, resulting in the formation of large agglomerates. Importantly, the resistant starch (RS) content was significantly increased by 24.05% and 37.04% in HMT combined with PAW and ANN combined with PAW, respectively, compared with NCF. These findings support the development of healthy and tasty functional foods and demonstrate a potential to modify the structure of corn flour, reduce starch digestibility, and increase RS content through a green pathway.