In this study, it is demonstrated that a finer nanostructure produced under a rapid rate of solvent removal significantly improves charge separation in a high-performance polymer:fullerene bulk-heterojunction blend. During spin-coating, variations in solvent evaporation rate give rise to lateral phase separation gradients with the degree of coarseness decreasing away from the center of rotation. As a result, across spin-coated thin films the photocurrent at the first interference maximum varies as much as 25%, which is much larger than any optical effect. This is investigated by combining information on the surface morphology of the active layer imaged by atomic force microscopy, the 3D nanostructure imaged by electron tomography, film formation during the spin coating process imaged by optical interference and photocurrent generation distribution in devices imaged by a scanning light pulse technique. The observation that the nanostructure of organic photovoltaic blends can strongly vary across spin-coated thin films will aid the design of solvent mixtures suitable for high molecular-weight polymers and of coating techniques amenable to large area processing.