Improving the fluidity of waxy oil with different pour point depressants (PPDs) at low temperature is of great technical and economic interest. In the present work, a nanocomposite pour point depressant (NPPD) which was developed based on melt blending of organically modified montmorillonite and ethylene/vinyl acetate (EVA) copolymer has been investigated systematically. The microscopic properties of waxy model oil with NPPD were investigated and compared with that of conventional EVA through X-ray diffraction. The interplanar spacing and lattice parameter are found to decrease in the (0 0 6) interplanar and z-axis for both NPPD and EVA, but display opposite trends between NPPD and EVA in (1 1 0), (2 0 0), x-axis. For NPPD, the wax appearance temperature (WAT) shows a slight increase with increasing concentration, while the crystallinity index (CI) accompanied with peak area in different crystal interplanar decreases. In EVA system, however, the WAT and CI present opposite trends. The NPPD behaves a dominated nucleation and a combination of co-crystallization with adsorption mechanism. This study provides a fundamental and microscopic perspective for the understanding of wax crystallization modification mechanism.