Heteroepitaxially grown multilayered thin film structures have been attracted of great interest due to its potential applications in photovoltaic/light emitting/electronics devices. The thin film morphology plays an important role in enhancing its related physical properties. It is not easy to simulate the multi-layered thin film structures due to the influence of the interface/surface fluctuation. However, the phase field method, based on thermodynamics and Cahn-Hilliard diffusion model, can predict the thin film morphologies without tracking the interfaces. In this paper, a new phase field model was developed for predicting multi-layer structures with multi-order parameters. The morphologies with strain distributions of the quantum wells, quantum dots and buffer layers structures were investigated in the current study. We found that the strain distribution has a strong effect on the suface/interface morphologies in the multilayered structures. Some simulation results are consistent with experimental observations.