A new simulation approach for combining hydration force with generalized Langevin dynamics is developed in this paper. The exponential model is taken for the friction kernel. The hydration force determined by the boundary elementary method is taken into account as the mean force terms of the solvent, including the Coulombic interactions with the induced surface charge and the surface pressure of solvent. All simulations were performed on cyclic undecapeptide cyclosporin A (CPA). The simulation results obtained using the new method were analyzed and compared with those obtained using other methods, such as molecular dynamics simulations, generalized Langevin dynamics simulations, and conventional stochastic dynamics simulations. We found that the results obtained with the new method presented in this study show obvious improvements over the other simulation techniques and that the hydration force and friction relaxation together contribute to this improvement.