This work concerns different cultivars of waxy maize starch (WMS), from which a significant correlation between the multi-scale structure and the digestibility has been identified. WMSs show a typical A-type crystalline polymorph. The surface porosity of WMS granules facilitates their digestibility. In contrast, the in vitro digestion results indicate that the resistant starch (RS) content increased with higher contents of amylose, single helices, and surface short-range ordered structures. Resistant starch (RS) was found to be made up of single helices and perfect crystallites formed by the fraction of chains with a degree of polymerization (DP) between 13 and 24. Slowly digestible starch (SDS) consists of single helices. Rapidly digestible starch (RDS) is mainly composed of disordered molecular chains in the amorphous regions of starch. This work reveals the relationship between the multiscale structure and digestibility of different WMSs and can provide guidance for the application of WMSs in food or non-food fields.