The interactions between starch and protein, the essential components of lotus seed, strongly influence the quality of lotus seed processing by-products. This study investigated the effects of lotus seed starch-protein (LS-LP) interactions on the structural, thermal and gelatinization properties of LS-LP mixtures, using LS/LP ratios of 6:1, 6:2, 6:3, 6:4, 6:5, or 1:1, after heat treatment (95 °C, 30 min). Fourier transform infrared peaks at 1540 cm and 3000-3600 cm revealed the major interactions (electrostatic and hydrogen bonding) between LS and LP. The UV-visible absorption intensities (200-240 nm) of LS-LP mixtures increased with increased protein content. X-ray diffraction and electron microscopy revealed that LS-LP consists of crystalline starch granules encapsulated by protein aggregates. Increasing the addition of protein to the mixtures restricted the swelling of the starch granules, based on their solubility, swelling properties and thermal properties. Viscometric analysis indicated that the formation of LS-LP mixtures improved structural and storage stability. These findings provide a practicable way to control the thermal and gelatinization properties of lotus seed starch-protein mixtures, by changing the proportions of the two components, and provide a theoretical basis for developing novel and functional lotus-seed-based foods.