Objective: This study aimed to investigate the formation mechanism of starch-lipid complex. Methods: Using different fatty acids with carbon chain length of C12~C18 to complex with debranched / non-debranched high amylose corn starch, by measuring the thermal properties, crystalline structure and ordered structure of the complexes with differential scanning calorimetry, X-ray diffraction, and Fourier transform infrared spectrometer, the effects of fatty acid chain length and debranched/non-debranched high amylose corn starch on the structure and properties of starch-fatty acid complexes were explored. Results: The compound degree of debranched starch and fatty acid decreased with the increase of carbon chain length, and the composite rate of lauric acid (15.00%) was found highest. The degree of composite of non-debranched starch and fatty acids increased first and then decreased with the increase of carbon chain length, and the composite rate of palmitic acid (13.73%) was the highest. The thermal properties, crystal structure and ordered structure of the complexes were related to the compound degree. After forming complexes with fatty acid, the crystal structure of high amylose corn starch changed from B-type to V-type. Conclusion: Fatty acid chain length and starch debranching had great influence on the structure and physicochemical properties of starch-lipid complex.