We have obtained high-resolution frictional force images of copper phthalocyanine (CuPc) crystals deposited on hydrogen-terminated Si(001)-(2 × 1) surfaces, which involve information on the details of the molecular arrangement. The crystal is found to have the same lattice constants as those of α-form crystals. Two possible monolayer packing models based on the lattice constants obtained are examined with a molecular mechanics simulation. A variation of the α-CuPc(001) monolayer model in which the inclination direction of the molecules alternates from column to column shows good agreement with the frictional force image. Molecular mechanics has been also used to explain the in-plane orientation of the CuPc crystals. The preferable orientational angle between the molecular column and the substrate 〈110〉 direction is estimated to be 16–17° simply by assuming the atom-atom van der Waals potentials. The calculated angle is in good agreement with the experimental results.