Microstructure and composition significantly influence the physical properties of thin films. Therefore, these can be adapted to enhance the functionality of thin films for practical applications. Herein, the anomalous microstructural evolution of sputtered GeO2 thin films based on postdepositional heat treatments is reported. Temperature‐dependent microstructural variations are investigated systematically via a combinatorial postdepositional heat treatment employing a natural thermal gradient in a tube furnace. Heat treatment under an oxidizing atmosphere results in a transition from the amorphous phase to the quartz phase, and subsequent heat treatments under a reducing atmosphere cause H2O‐incorporated chemical reactions. Hence, these conditions create unique microstructural features and yield optical transmittance variations in the GeO2 thin films. The phase transition induces the formation of spherulitic hexagonal GeO2 crystallites, and further increase in the temperature promotes the agglomeration of crystallites in the amorphous matrix. The incorporation of H2O results in the growth of the microstructure, and the chemical reduction to Ge metal begins to generate small granules from the boundary of the microstructures. The experimental results and proposed mechanisms presented herein for the microstructural and compositional changes serve as references for designing the physical properties of thin films.