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We investigated the structural and optical properties of Cu-poor CuGaSe2 (CGSe) films depending on the use of different substrates: indium-doped tin oxide (ITO) coated soda-lime glass (SLG) and fluorine-doped tin oxide (FTO) coated SLG as back contacts, widely used Mo-coated SLG, and pure SLG. The Cu-poor phase is chosen as a counterpart of Cu-poor Cu(In,Ga)Se2 to show the highest efficiency in this class of materials, and also give a test board for parasitic phases which might influence on device properties. Although the Cu-poor CGSe thin-films were deposited on the four substrates at the same time in an identical condition, they showed differences in the morphology and grain size due to different CGSe/substrate interfaces and growth mechanisms depending on the substrates. These surface properties of the CGSe films were identified clearly by atomic force microscopy (AFM) measurements. X-ray diffraction (XRD) measurement also supported the result of the AFM analysis and showed that the preferred orientation of CGSe is (112), independent of the substrates. The existence of parasitic phases was examined by Raman and photoluminescence spectroscopic techniques. While defect compounds such as CuGa3Se5 and CuGa5Se8 were identified for all films, the signals related to these parasitic phases are strongest for the films on the pure SLG substrate. Furthermore, the absorption property was investigated by spectroscopic ellipsometry in a photon energy range of 0.7–5 eV. We found that the absorption coefficient values for the CGSe films are about 104–105 cm−1 in the visible region. The absorption coefficient is also changed according to the use of different substrates. This difference comes from the parasitic phase formation, which leads to an increase of the bandgap and suppression of the optical absorption strength. Our systematic study suggests clearly that the difference in distribution of parasitic phases in the CGSe films could originate primarily from the different substrates used for the film deposition.