We present structural studies of the spin-1/2 honeycomb-lattice antiferromagnet, Cu-2(pymca)(3)(ClO4) (pymca: pyrimidine-2-carboxylate), using synchrotron X-ray diffraction experiments. Previous research reported that its crystal structure consists of a regular honeycomb lattice, which exhibits quantum spin-liquid behavior. However, due to its threefold Cu2+ site symmetry, this proposed crystal structure cannot describe Jahn-Teller distortion. We analyzed the structure of Cu-2(pymca)(3)(ClO4), including superlattice reflections that were overlooked during previous X-ray diffraction studies of the material, and clarified that its distorted honeycomb lattice consists of Cu-2(pymca)(3) sections. Further investigation of Cu-2(pymca)(3)(ClO4) crystal structure may reveal magnetic susceptibilities of the distorted honeycomb lattice.