Understanding the morphology of polymer-based bulk heterojunction (BHJ) solar cells is necessary to improve device efficiencies. Blends of a low-bandgap silole-containing conjugated polymer, poly[(4,4′-bis(2-ethylhexyl)dithieno[3,2-b;2′,3′-d]silole)-2,6-diyl-alt-(4,7-bis(2-thienyl)-2,1,3-benzothiadiazole)-5,5′-diyl] (PSBTBT) with [6,6]phenyl-C61-butyric acid methyl ester (PCBM) were investigated under different processing conditions. The surface morphologies and vertical segregation of the “As-Spun”, “Pre-Annealed”, and “Post-Annealed” films were studied by scanning force microscopy, contact angle measurements, X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, dynamic secondary ion mass spectrometry, and neutron reflectivity. The results showed that PSBTBT was enriched at the cathode interface in the “As-Spun” films and thermal annealing increased the segregation of PSBTBT to the free surface, while thermal annealing after deposition of the cathode increased the PCBM concentration at the cathode interface. Grazing-incidence X-ray diffraction and small-angle neutron scattering showed that the crystallization of PSBTBT and segregation of PCBM occurred during spin coating, and thermal annealing increased the ordering of PSBTBT and enhanced the segregation of the PCBM, forming domains ∼10 nm in size, leading to an improvement in photovoltaic performance.