Understanding the structural characteristics of starch can help in determining its functional properties and choosing appropriate applications. This work aimed to comprehensively characterize and understand the morphological, crystalline, and molecular structure of the normal and waxy wheat A- and B- starch granules. X-ray diffraction analysis revealed that both normal and waxy wheat A- and B- starch granules have a typical A-type crystalline structure. Additionally, scanning electron microscopy, small-angle X-ray scattering, and Fourier transform infrared spectroscopy analyses showed differences in shape, the thickness of semi-crystalline growth rings, and short-range molecular order of the normal and waxy A- and B- starch granules. The wheat A-starch granules contained lower proportions of A-chains (DP 6–12) and B1- chains (DP 13–24) than those of the wheat B- starch granules. Also, the results revealed that B1-chains (DP 13–24) play an important role in the formation of surface/mass fractal characteristics of starch granules. Furthermore, the atomic force microscopy analysis showed that the normal and waxy wheat A-starch granules are mass fractal, while the normal and waxy wheat B- starch granules are surface fractal.