Domain purity and interface structure are known to be critical for fullerene-based bulk heterojunction (BHJ) solar cells, yet have been very difficult to study. Using novel soft X-ray tools, we delineate the importance of these parameters by comparing high performance cells based on a novel naphtha[1,2-c:5,6-c]bis[1,2,5]thiadiazole (NT) material to cells based on a 2,1,3-benzothiadiazole (BT) analogue. BT-based devices exhibit ∼15 nm, mixed domains that differ in composition by at most 22%, causing substantial bimolecular recombination. In contrast, NT-based devices have more pure domains that are >80 nm in size, yet the polymer-rich phase still contains at least 22% fullerene. Power conversion efficiency >6% is achieved for NT devices despite a domain size much larger than the nominal exciton diffusion length due to a favourable trade-off in the mixed domain between exciton harvesting, charge transport, and bimolecular recombination. The miscibility of the fullerene with the NT and BT polymer is measured and correlated to the purity in devices. Importantly, polarized x-ray scattering reveals preferential face-on orientation of the NT polymer relative to the PCBM-rich domains. Such ordering has previously not been observed in fullerene-based solar cells and is shown here to be possibly a controlling or contributing factor to high performance.