Crystallization of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) in thin films and in blend films with various polymers was investigated by X-ray diffraction. Thermal annealing induced the crystallization of PCBM in the blend films only through direct contact with a crystallized pure PCBM layer beneath, suggesting that an epitaxial crystallite growth occurred from the bottom interface. The morphology of the crystals depended strongly on the mixing ratio and the crystal structure of the bottom layer, and nanorod-like PCBM crystallites with widths in the range of 100–150 nm and lengths in the range of 150–500 nm were observed. A bulk-heterojunction (BHJ) organic solar cell utilizing the PCBM crystallite as the acceptor showed the highest VOC of 0.83 V for a PTB7:PCBM device to date. These findings offer the ways to use the crystallized PCBM with the controlled nanostructures as the electron conducting materials in organic and hybrid perovskite photovoltaics.