From a structural analysis using low-energy ion scattering spectroscopy, it is shown that Cu-phthalocyanine (CuPc) molecules adsorb on the Fe(100) surface with their planes parallel to the surface when the film thickness is one monolayer, while the structure of the film becomes disordered with an increase in the thickness. This thickness dependence of the CuPc film structure agrees with that determined from the metastable deexcitation spectroscopy (MDS) spectra, and the origins of the CuPc peaks in the MDS spectra are determined. The spin polarization in the molecular orbitals of CuPc on Fe is detected by spin-polarized MDS (SPMDS). The polarity of the spin polarization in the CuPc molecular orbitals is the same as that of the Fe surface. The adsorption of oxygen on Fe prior to the CuPc deposition is found to induce a remarkable difference in the spin polarization of the CuPc orbitals.