The nutritional functions of resistant starch (RS) are closely related to its gut fermentation processes. The aim of this study was to explore the relationship between in vitro digestion and fermentation characteristics of heat moisture treatment induced chestnut starch-lipid (oleic acid; linoleic acid; maize oil) complexes from perspective of ordered structural changes during simulated digestion process. The results showed the formation of ordered structures differed significantly among three complexes with similar RS content (∼40%), while their ordered structures decreased significantly after digestion. In contrast to chestnut starch, starch-lipid complexes could successfully encourage the production of healthy gut bacteria, and the difference in total ordered structure was the key factor in the generation of total short-chain fatty acids especially propionate during fermentation. Interestingly, correlation analysis found the presence of V-type complex might facilitate the proliferation of acetate-produced microbiota especially Lactobacillus, Lactococcus, and Bifidobacterium to produce acetate. Our findings could provide basic data on the creation of starch-based functional ingredients for optimal gut health.