The filler size-dependent elastic stiffness of nanosilica (α-quartz)-reinforced polyimide(s-BPDA/1,3,4-APB) composites under the same volume fraction and grafting ratio conditions was investigated via molecular dynamics(MD) simulations. To enhance the interfacial load transfer efficiency, we treated the surface oxygen atoms of the silica nanoparticle with additional silicon atoms attached by a propyl group to which the aromatic hydrocarbon in the polyimide is directly grafted. As the radius of the embedded nanoparticle increases, the Young's and shear moduli gradually decrease, showing a prominent filler size effect. At the same time, the moduli of the nanocomposites increase as the grafting ratio increases. The contribution of different nanoparticles to the filler size dependency in elastic stiffness of the nanocomposites can be elucidated by comparing the normalized adhesive interaction energy between the particle and matrix which exhibits prominent filler size dependency. Because of the immobilization of the matrix polymer in the vicinity of the nanoparticles, which was confirmed by the self-diffusion coefficient, the highly grafted interface is found to bring about a greater reinforcing effect than the ungrafted interface.