We propose a new method to form small-molecule based bulk heterojunctions (SM-BHJs) through alternative thermal deposition (ATD), which is a simple modification of conventional thermal evaporation. By ATD, the thicknesses of alternative donor and acceptor layers are precisely controlled down to 0.1 nm, which is critical to form BHJs. The formation of a BHJ in copper(II) phthalocyanine (CuPc) and fullerene (C-60) systems is confirmed by atomic force microscopy (AFM), grazing incidence X-ray small angle scattering (GISAXS), and absorption measurements. From analysis of the data, we find that the CuPc|C-60 films fabricated by ATD are composed of nanometer sized disk-shaped CuPc nano grains and aggregated C-60, which explains the phase separation of CuPc and C-60. On the other hand, the co-deposited CuPc: C-60 films do not show the existence of separated CuPc nano grains in the CuPc: C-60 matrix. The OPV cells fabricated using the ATD method show significantly enhanced power conversion efficiency compared to the co-deposited OPV cells with the same composition.