Time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra of polystyrene (PS) films supported on silicon wafers were obtained at temperatures ranging from room temperature to 100 °C. Principal component analysis (PCA) of the TOF-SIMS data revealed a transition temperature (TT) at which the surface structure of PS was rearranged. The TT of a 120-nm thick PS (weight-average molecular weight of 3,000 g/mol) thin film was determined to be about 36 °C, which is approximately 30 °C lower than the bulk glass transition temperature (Tg) of that PS. Similar TTs were observed on PSs with different molecular weights. As the TT is strongly related to the Tg and dependent on the molecular weight, it is believed that the TT determined by TOF-SIMS is related to the surface glass transition temperature (Tg(S)) measured by other techniques. This suggests that TOF-SIMS combined with PCA can be used to determine the Tg(S) of polymer films. Furthermore, the detailed PCA analyses indicate that the phenyl groups of PS tended to move away from the surface at temperatures above TT. This conclusion was further confirmed by contact angle and XPS measurements.