The soybean peptide-starch complex was prepared using microwave-assisted treatment. The effects of microwave power levels at 350, 550, 700 and 1000 W on the interactions between soybean peptides and three types of starch—sweet potato, corn starch, and caltrop starch—were systematically investigated. The structure, physicochemical properties, and digestibility of the as-prepared complexes were explored. The results showed that compared with the physical mixture of starch, the soybean peptide-starch complex subjected to microwave treatment exhibited significant structural and functional changes. Scanning electron microscopy revealed the formation of a porous gel network along with aggregate structure, accompanied by a notable increase in particle size. X-ray diffraction and Fourier transform infrared spectroscopy (FT-IR) analyses demonstrated a reduction in crystallinity, characterized by a contraction of the crystalline peak at 1047 cm⁻¹/1022 cm⁻¹, while the amorphous region at 1022 cm⁻¹/995 cm⁻¹ remained relatively unchanged. Functionally, the complex displayed reduced gel strength and hardness, diminished anti-aging properties, yet improved freeze-thaw stability. In vitro digestion studies indicated that, compared to the physical mixture of soybean peptides and starch, the microwave-treated complex contained significantly lower levels of rapidly digestible starch. Notably, samples treated with 700 W microwave irradiation showed marked increases in both slowly digestible starch and resistant starch content, up to 28.20% and 35.70%, respectively. This study provides valuable insights into the development of soybean peptide-starch complexes and supports the potential application of modified starch as a hypoglycemic ingredient in food and frozen food products.