The structural and digestive properties of indica rice starch-fatty acid complexes and the effects of lipoxygenase on the structural and digestive properties of the complexes were examined in this study. The complexes were characterized by scanning electron microscopy, X-ray diffraction, Fourier transform-infrared spectroscopy and Raman spectroscopy. The results showed that indica rice starch had the highest molecular chain order and the highest crystallinity, and the crystallization disappeared after gelatinization, and the formation of indica rice starch-fatty acid complexes promoted the transformation of starch crystal structure from A-type to V-type. Lipoxygenase reduced the regularity of starch molecular crystal structure in the complexes, while enzyme protein improved the order of starch molecular structure in the complexes. The regularity of starch crystal structure in the complexes could improve with the increase of composite temperature and the increase of fatty acid unsaturation. In vitro digestibility and in vitro digestion kinetics showed that the formation of indica rice starch-fatty acid complexes reduced the digestibility of indica rice starch to a certain extent. The RDS content of indica rice starch was 66.42 ± 0.39 %, and lipoxygenase reduced the reduction of rapidly digested starch content during complexes digestion, while enzyme protein increased the content of resistant starch.