Starch-lipid complexes were prepared using lotus seed starch (LS) and glycerin monostearate (GMS) via a high-pressure homogenization process, and the effect of high pressure homogenization (HPH) on the slow digestion properties of LS-GMS was investigated. The digestion profiles showed HPH treatment reduced the digestive rate of LS-GMS, and the extent of this change was dependent on homogenized pressure. Scanning electron microscopy displayed HPH treatment change the morphology of LS-GMS, with high pressure producing more compact block-shape structure to resist enzyme digestion. The results of Gel-permeation chromatography and Small-angle X-ray scattering revealed high homogenization pressure impacted molecular weight distribution and semi-crystalline region of complexes, resulting in the formation of new semi-crystalline with repeat unit distance of 16–18 nm and molecular weight distribution of 2.50–2.80 × 105 Da, which displayed strong enzymatic resistance. Differential scanning calorimeter results revealed new semi-crystalline lamellar may originate from type-II complexes that exhibited a high transition temperature.