The melting and crystallization behaviors of poly(ε-caprolactone) (PCL) ultra-thin films with thickness from 15 nm to 8 nm were studied by AFM technique equipped with a hot-stage in real-time. It was found that melting can erase the spherulitic structure for polymer film with high thickness. However, annealing above the melting point can not completely erase the tree-like structure for the thinner polymer film. Generally, the structure formation of thin polymer films of PCL is controlled not only by melting and crystallization but also by dewetting during thermal annealing procedures, and dewetting predominates in the structure formation of ultra-thin films. However, the presence of tree-like morphology at 75 °C may be due to the strong interaction between PCL and mica surface, which may stick the PCL chains onto the mica surface during thermal annealing process. Moreover, the growth of the dendrites was investigated and it was found that crystallization is followed from a dewetted sample, and the branches did not grow with the stems. The crystallization of polymer in the ultra-thin films is a diffusion-controlled process. Both melting and crystallization behaviors of PCL in thin films are influenced by film thickness. The melting and crystallization behaviors of poly (ε-caprolactone) (PCL) ultra-thin films with thickness from 15 nm to 8 nm were studied by AFM technique equipped with a hot-stage in real-time. It was found that melting can erase The spherulitic structure for polymer film with high thickness. However, annealing above the melting point can not completely erase the tree-like structure for the thinner polymer film. crystallization but also by dewetting during thermal annealing procedures, and dewetting predominates in the structure formation of ultra-thin films. However, the presence of tree-like morphology at 75 ° C may be due to the strong interaction between PCL and mica surface, which may stick the PCL chains onto the mica surface during thermal annealing process. Moreover, the growth of the dendrites was investigated and it was found that crystallization is followed from a dewetted s ample, and the branches did not grow with the stems. The crystallization of polymer in the ultra-thin films is a diffusion-controlled process. Both melting and crystallization behaviors of PCL in thin films are influenced by film thickness.