We employ analytical transmission electron microscopy (TEM) to correlate the structural and chemical environment variations within a stacked epitaxial thin film of the high entropy oxide (HEO) Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O (J14), with two layers grown at different substrate temperatures (500 and 200 °C) using pulsed laser deposition (PLD). Electron diffraction and atomically resolved STEM imaging reveal the difference in out-of-plane lattice parameters in the stacked thin film, which is further quantified on a larger scale using four-dimensional STEM (4D-STEM). In the layer deposited at a lower temperature, electron energy loss spectroscopy (EELS) mapping indicates drastic changes in the oxidation states and bonding environment for Co ions, and energy-dispersive X-ray spectroscopy (EDX) mapping detects more significant cation deficiency. Ab initio density functional theory (DFT) calculations validate that vacancies on the cation sublattice of J14 result in significant electronic and structural changes. The experimental and computational analyses indicate that low temperatures during film growth result in cation deficiency, an altered chemical environment, and reduced lattice parameters while maintaining a single phase. Our results demonstrate that the complex correlation of configurational entropy, kinetics, and thermodynamics can be utilized for accessing a range of metastable configurations in HEO materials without altering cation proportions, enabling further engineering of functional properties of HEO materials.