As a type of phytoestrogen, lignans have attracted attention in recent years for their nutritional functions. To investigate the effects of lignans on the structural and nutritional functions of starch, honokiol (HK) and arctiin (AC) were complexed with rice starch respectively under high-pressure homogenization (UHPH) (UHPHRS/HK and UHPHRS/AC). The results showed that both HK and AC could form inclusive complexes with rice starch via non-covalent bonding (hydrophobic interaction and hydrogen bonds), and these complexes could further form V-type crystals and aggregates, which reduced the starch digestibility as well as endowing them with the ability to retard glucose release and bind sodium cholate. Interestingly, due to its smaller molecular size, HK could induce starch to form a more compact structure than AC, leading to better nutritional functions. When the addition of HK/AC reached 8%, the resistant starch content could reach 26% and 19.8%, respectively. Meanwhile, the glucose dialysis retardation index could increase to 17.2% and 14.8%, respectively, and the sodium cholate-binding capacity could increase to 33.1 mg g⁻¹ and 21.8 mg g⁻¹, respectively. These results demonstrated that UHPH with lignans’ molecular interaction could be beneficial for controlling the nutritional functions of starch products with the desired digestibility.