The self-assembly of the binary molecular system comprising copper(II) phthalocyanine (CuPC) and copper-hexadecafluoro-phthalocyanine (F16CuPC) on graphite has been investigated by in situ low-temperature scanning tunneling microscopy (LT-STM). The adsorption of this binary molecular system on graphite results in the formation of a well-ordered chessboardlike nanopattern. The in-plane molecular orientation of the guest CuPC molecules can be tuned by varying the coverage. At low coverage, the sparse CuPc molecules are randomly embedded in the host F16CuPc monolayer, possessing two different in-plane orientations: as the CuPC coverage increases, the in-plane molecular orientations of CuPc and F16CuPc become unidirectional and a highly ordered chessboardlike pattern forms. Molecular dynamic (MD) simulation results suggest that the selective and directional intermolecular hydrogen bonding determines the in-plane molecular orientation as well as the supramolecular packing arrangement .