Scandium (Sc) and yttrium (Y) co-doped ZrO2 (ScYSZ) thin films were prepared on a SiO2-Si substrate via pulsed laser deposition (PLD) method. In order to obtain good quality thin films with the desired microstructure, various oxygen partial pressures (PO2) from 0.01 Pa to 10 Pa and substrate temperatures (Ts) from 25 °C to 800 °C were investigated. X-ray diffraction (XRD) patterns results showed that amorphous ScYSZ thin films were formed at room substrate temperature while cubic polycrystalline thin films were obtained at higher substrate temperatures (Ts = 200 °C, 400 °C, 600 °C, 800 °C). Raman spectra revealed a distinct Raman shift at around 600 cm−1 supporting a cubic phase. However, a transition from cubic to tetragonal phase can be observed with increasing oxygen partial pressure. Photoemission spectroscopy (PES) spectra suggested supporting analysis that more oxygen vacancies in the lattice can be observed for samples deposited at lower oxygen partial pressures resulting in a cubic structure with higher dopant cation binding energies as compared to the tetragonal structure observed at higher oxygen partial pressure. On the other hand, dense morphologies can be obtained at lower PO2 (0.01 Pa and 0.1 Pa) while more porous morphologies can be obtained at higher PO2 (1.0 Pa and 10 Pa).