Starch-fatty acid complexes have attracted much attention as a type of novel resistant starches due to the formation of V-amylose between amylose and fatty acids. The aim of the present study was to investigate the structure and properties of different starch-fatty acid complexes, including size and shapes of nanoscale supramolecular structures formed through hydrothermal treatment. The molecular attributes were studied using X-ray diffraction (XRD), ultra small-angle X-ray scattering (USAXS), small-angle X-ray scattering (SAXS) and scanning electron microscopy (SEM) techniques. Results from optical microscopy and SEM analyses showed that starch-fatty acid complexes remained the Maltese cross and granular morphology of native starch. XRD revealed the crystalline morphology of starch-fatty acid complexes with B-type and V-type crystalline structures. The crystallinities of the complexes varied depending on the fatty acid and method used. USAXS/SAXS experiments demonstrated that fatty acid chain length and level of saturation affected both the lamellar structure and the B-type crystalline structure of the complexes. Moreover, the processing methods also exhibited significant influence on the nanostructure of complexes. Overall, this study contributes to the understanding of the structure and properties of amylose-fatty acid resistant starch, which may facilitate the future design and fabrication of such systems.