Self-assembly allows new opportunities to control the morphology and properties of fullerene-based materials. By using the electron-accepting underivatized C-60 and electron-donating pyridine groups of a polystyrene-block-poly(4-vinylpyridine), PS-block-P4VP, we here show the first example that charge-transfer complexation between fullerenes and block copolymers can essentially modify the self-assembled structures. The morphology of C-60/PS-block-P4VP mixture is studied in both bulk and thin films by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) upon casting from freshly prepared or differently aged xylene solutions. Selecting PS-block-P4VP that leads to hexagonal self-assembly with P4VP cylindrical cores, closely similar cylindrical structure is observed upon adding a small amount of C60, when freshly prepared xylene solutions are used to cast solid bulk or thin film samples. In this case the C60 molecules swell the PS matrix. By contrast, spherical morphology is observed if aged xylene solutions have been used where C60 has slowly penetrated into the P4VP micellar cores due to charge-transfer complexation, as evidenced by UV-vis and FTIR spectroscopy. This morphological change is unexpected, as according to simple block copolymer theory selective incorporation of a small molecular species or nanoparticles within the minority block of hexagonally self-assembled cylindrical diblock copolymer system should render the morphology toward lamellar structures. This suggests that charge-transfer complexation can be relevant in considering the self-assembled structures of block copolymers and fullerenes.