Copper phthalocyanine (CuPc) films were grown on Si(001) substrates at temperatures between 483 K and 150 K by organic molecular beam deposition under ultra-high vacuum of 1 × 10−7 Pa. The X-ray diffraction (XRD) measurement and the atomic force microscope (AFM) lattice image observation revealed that a-axis oriented α -CuPc columnar crystals were epitaxially grown on Si(001) at substrate temperature (Ts) between 363 and 453 K. The b (c) axis of the α-CuPc crystal was parallel to the Si [110] (Si [11¯0]). Very smooth α-CuPc film was also prepared at 150 K. The root-mean-square roughness obtained from the AFM measurement was 0.89 nm. The phase of polymorphs of CuPc was determined by Fourier transform infrared spectroscopy with a standard powder transmission measurement. The electron spin resonance investigation indicates that the molecular plane is tilted at an angle of 21 ± 3 ° with respect to the substrate surface. A CuPc film was also deposited on the surface of a Langmuir—Blodgett film on glass, and investigated by XRD and AFM. The substrate suppresses the epitaxial columnar crystal growth even at high temperature.