Strain can be used to modulate magnetic properties of manganite thin film by affecting not only its crystal structure but also the microstructure, including the cluster size and fraction of ferromagnetic phase. In this work, epitaxial Pr0.67Sr0.33MnO3 thin films deposited on (001)-SrTiO3 single-crystal substrate are studied. The magnetization-temperature curves with zero-field cooling and field cooling show the typical feature of cluster-glass system. With the increase of film thickness, strain relaxation occurs in 80 nm Pr0.67Sr0.33MnO3 film with a wide temperature range of phase transition. By fitting the freezing temperature Tf dependence on magnetic field according to Almeida–Thouless equation, the 80 nm film has a larger local anisotropy and exchange bias compared to that of the 15 nm Pr0.67Sr0.33MnO3 film. Detailed analysis suggests that the strain-induced phase fraction and size distribution of ferromagnetic phase are responsible for the different magnetic properties of Pr0.67Sr0.33MnO3 film with different thickness.