The effects of plasma treatment on the multi-scale structure and in vitro digestibility of maize starch with different amylose contents were systematically evaluated. The results demonstrated that all maize starches' molecular weights (MW) decreased when treated with plasma, among which the MW of waxy maize starch displayed the largest reduction. Plasma treatment led to an increase in the thickness of the semi-crystalline lamellae and double helix proportions of waxy and normal maize starches. However, high-amylose maize starch presented a less ordered structure by plasma treatment. Additionally, larger pores and channels were observed on the surface of plasma-treated waxy and normal maize starch granules. Moreover, deposits were displayed on the surface of high-amylose maize starch granules. These changes increased the in vitro digestibility and hydrolysis rate of three starches after plasma treatment. Notably, plasma treatment caused diverse alterations in the structure and functionality of maize starch varying in amylose content, leading to maize starch with better digestibility, therefore being used as an ingredient for functional foods.