Self-assemblies of a nonplanar dysprosium-phthalocyanine (DyPc) molecule on the reconstructed Au(111) substrate have been examined with a low-temperature scanning tunneling microscope (STM). A four-lobed structure with a dark center hole is imaged as an isolated DyPc molecule, where the Dy atom is expected to be positioned below the Pc plane and bound to the Au substrate. Careful measurements reveal that the axes of isolated DyPc molecules align well with the high symmetry directions of Au. This fact illustrates a strong molecule-substrate interaction. In a monolayer film, a square molecule lattice is observed, where the geometries of the molecules can be determined by our submolecularly resolved STM images. The deduced lattice vectors and the azimuthal angles of the molecules account for a dominant molecule-molecule interaction. In a bilayer growth regime, the bonding configurations of the molecules in the second layer coincide with that of the first layer. A similar azimuthal angle appearing in the two layers may indicate a columnar packing geometry of DyPc molecules.