Polyamide 66 (PA66) was chosen as the representative of hydrophilic polymers, to investigate the influence of epitaxial crystals in semi-crystalline polymers/reduced graphene oxide nanocomposite injection-molding bars. A differential scanning calorimeter was used, and the two-dimensional wide-angle X-ray diffraction technique, as well as the two-dimensional small angle X-ray scattering technique, were used to research the crystallization behavior in PA66/RGO nanocomposites. The results indicated that RGO was an effective nucleation agent for PA66. The presence of RGO could enhance the orientation degree of the PA66 crystals and did not influence the crystal structure of the PA66. The non-epitaxial crystals and the epitaxial crystals existed in PA66/RGO nanocomposites. The size of epitaxial crystals was much greater than that of the non-epitaxial crystals. Tensile test results showed that the presence of fewer epitaxial crystals can improve the mechanical properties of a polymer.