Fluorite-structure binary oxides (e.g., HfO₂ and ZrO₂) have attracted increasing interest for a broad range of applications including thermal barrier coatings, high-k dielectrics, and novel ferroelectrics. A crystalline structure plays a crucial role in determining physical and chemical properties. Structure evolution of ZrO₂ thin films, particularly down to the nanometer scale, has not been thoroughly studied. In this work, we carried out systematic annealing analysis on the ZrO₂ thin films. Through in-situ high-temperature X-ray diffraction (XRD) characterizations, a thickness dependence of crystallization and phase transition is observed. Irrespective of the thickness (10–300 nm), the as-prepared amorphous ZrO₂ thin films are preferentially crystallized into a tetragonal (t) structure (high-temperature phase), which can be preserved down to room temperature (RT) upon annealing at the corresponding crystallization temperature (T_C). When annealing at temperatures higher than T_C, the transition from t to monoclinic (m; RT phase) will occur, and the quantity of the transition strongly depends on the film thickness. Our work expands the basic understanding of the phase transition in the ZrO₂ thin films, and offers a path to the selective control over the phase structure for novel functionalities.