The nutritional design of personalized starchy foods has become a research hotspot in the field of food science. Driven by the immense functional and nutritional implications of starch-lipid binary interactions, this study is aimed at designing starch digestibility by controlling the interaction between starch and glycerol monostearate (GMS)/stearic acid (SA) using a hot-extrusion 3D printing (HE-3DP) environment. The results indicated that the thermal shear force in the HE-3DP environment promoted hydrophobic interactions between starch and lipids, forming a V-type starch-lipid complex with a compact and ordered structure, thus enhancing enzymatic resistance. Compared with GMS, SA with linear hydrophobic chains was inclined to compound with starch to form a more ordered structure. Interestingly, the slowly digestible starch (SDS) and resistant starch (RS) content reached 25.06% when the added SA content was 10%. Besides, correlations between the structural parameters and digestibility were established, which provided crucial information for designing nutritional starchy food systems using HE-3DP.