The efficiency of polymer solar cells critically depends on the intimacy of mixing of the donor and acceptor semiconductors used in these devices to create charges and on the presence of unhindered percolation pathways in the individual components to transport holes and electrons. The visualization of these bulk heterojunction morphologies in three dimensions has been challenging and has hampered progress in this area. Here, we spatially resolve the morphology of 2%-efficient hybrid solar cells consisting of poly(3-hexylthiophene) as the donor and ZnO as the acceptor in the nanometre range by electron tomography. The morphology is statistically analysed for spherical contact distance and percolation pathways. Together with solving the three-dimensional exciton-diffusion equation, a consistent and quantitative correlation between solar-cell performance, photophysical data and the three-dimensional morphology has been obtained for devices with different layer thicknesses that enables differentiating between generation and transport as limiting factors to performance.