Two different fluorine-doped tin oxide (FTO)-coated glass substrates were investigated to find better suitability for CdTe solar cells. Substrate A consisted of FTO (300 nm)/SiO2 (24 nm)/intrinsic SnO2 (30 nm)/borosilicate glass (2.2 mm), and substrate B consisted of FTO (700 nm)/intrinsic SnO2 (30nm)/borosilicate glass (1.8 mm). The overall thickness of the FTO/glass substrates was about 2.5 mm. The total light transmittance of substrate B was much higher than that of substrate A throughout the whole spectral region, even though the thickness of the FTO in substrate B was twice larger than that of the FTO in the substrate A. The short-circuit current greatly increased in substrate B and the external quantum efficiency (EQE) increased over the whole wavelength range. This study shows that the diffuse optical transmittance played a key role in the large EQE value in the blue wavelength region, and the direct ransmittance played a key role in the large EQE value in the red wavelength region. The higher transmittance is due to the rough surface generated by the thicker FTO on glass. The conversion efficiency of the CdTe solar cell increased from 12.4 to 15.1% in combination of rough FTO substrate and Cu solution back contact.