Due to its excellent biocompatibility, high‐temperature resistance, chemical corrosion resistance, radiation resistance, and ease of processing and shaping, polyether ether ketone (PEEK) has been widely used in the field of oral medicine. In this study, we conducted an in‐depth investigation of the thermal annealing process of PEEK films at different temperatures. The grazing incidence wide‐angle x‐ray scattering (GIWAXS) results indicate that the PEEK molecular chains tend to align in an edge‐on orientation in the film, and annealing at different temperatures leads to the formation of two crystalline phases, A and B, with a spacing of 4.46 Å for (200) A and 4.69 Å for (200) B. The crystallization behavior during the annealing process was characterized using in situ GIWAXS, revealing an increase in the film's crystallinity in the early stages of annealing. Due to enhanced polymer chains mobility, the B phase is formed. However, during annealing at 200°C, the intensity of the (200) B peak initially increases and then decreases, indicating the instability of the B phase, which can be disrupted by excessive molecular mobility. Mechanical property characterization results demonstrate that as the annealing temperature increases, the film's elongation at break and modulus decrease.