Effects of chemical modification of wood with innovative ionic liquid on the supermolecular and morphology of wood/polypropylene composites were investigated using X-ray diffraction, hot stage optical microscopy, and differential scanning calorimetry. For the first time the chemical treatment of wood was conducted solely with newly synthesized ionic liquid, didecyldimethylammonium bis(trifluoromethylsulfonyl)imide. The modification was found to be responsible for significant changes in nucleating abilities of wood in polypropylene matrix. These findings were confirmed by crystallization temperature, crystal conversion, crystallization half-time parameters, as well as observation of transcrystalline structures. Ionic liquid treatment of wood influenced also formation of polymorphic forms of polymer matrix. In contrast to composites with untreated wood, in composites with modified wood filler formation of b-phase of polypropylene was observed. This fact was discussed in view of differences in nucleating activity of lignocellulosic filler, resulting from chemical treatment with ionic liquid. Moreover, a relationship between mechanical properties of composites and the phenomena taking place at the polymer-filler interface, controlled by chemical modifications of lignocellulosic components, was evaluated.