A morphologically stable bulk heterojunction (BHJ) with a large heterojunction area is prepared by reducing the portion of the small band gap polymer (PTB7) and fullerene intermixture through a sequential deposition (SqD) of the nanostructured PTB7 and the fullerene layer. The nanostructured PTB7 layer is prepared using a ternary solvent composed of chlorobenzene, 1,8-diiodooctane (DIO) and 1-chloronaphthalene (1-CN). Adding DIO and 1-CN enhances the ordering of PTB7 chains and results in a nanostructured polymer surface. The grazing incidence X-ray diffraction results reveal that the SqD of the nanostructured PTB7 and fullerene layers forms the BHJ with little intermixing between the polymer and the fullerene domains compared to the BHJ formed by the deposition of the blended PTB7 and fullerene solution (BSD). The OPV utilizing the SqD processed BHJ (SqD-OPV) exhibits a power conversion efficiency (PCE) of 7.43%, which is similar to that when the BSD processed BHJ (BSD-OPV) is utilized. Furthermore, the SqD-OPV exhibits an excellent thermal stability. The SqD-OPV maintains its initial PCE even after thermal annealing at 140 °C for 10 days, whereas the BSD-OPV maintains 78% of its initial efficiency under the same condition.