As compared with exogenous components, non-starch components (NSCS), such as proteins, lipids, non-starch polysaccharides (NSPs), and polyphenols, inherently present in cereals, are more effective at inhibiting starch digestibility. Existing research has mostly focused on complex systems but overlooked the analysis of the in-situ role of the NSCS. This study reviews the crucial mechanisms by which endogenous NSCS inhibit starch digestion, emphasizing the spatial distribution-function relationship. Starch granules are filled with pores/channels-associated proteins and lipids, embedding in the protein matrix, and maintained by endosperm cell walls. The potential starch digestion inhibition of endogenous NSCS is achieved by altering starch gelatinization, molecular structure, digestive enzyme activity, and accessibility. Starch gelatinization is constrained by endogenous NSCS, particularly cell wall NSPs and matrix proteins. The stability of the starch crystal structure is enhanced by the proteins and lipids distributed in the starch granule pores and channels. Endogenous polyphenols greatly inhibit digestive enzymes and participate in the cross-linking of NSPs in the cell wall space, which together constitute a physical barrier that hinders amylase diffusion. Additionally, the spatial entanglement of NSCS and starch under heat and non-heat processing conditions reduces starch accessibility. This review provides novel evidence for the health benefits of whole cereals.