The formation of a series of Xe-CuEtiol [Cu(II) etioporphyrin I] complexes on Cu(001) surface was identified by scanning tunneling microscopy (STM) at cryogenic condition. The binding sites of xenon to CuEtiol molecule were directly revealed by high-resolution STM images in combination with controlled manipulation. The interaction between xenon atoms and CuEtiol in the on-top configuration is suggestive of a charge-induced dipole interaction. The structural parameters obtained with the STM complement results from spectroscopic studies of van der Waals complexes.