Proton transport plays an important role in biological energy transduction and sensory systems. A multi-scale model is introduced to study the proton transport in membrane channels. Quantum dynamics in utilized to model the motion of target particle (protons), while multi-scale treatments are given to surrounding environments in classical mechanics, upon the priorities of interests and importance. All the system components are assembled on an equal footing in a total energy framework, from which the generalized Poisson-Boltzmann, Kohn-Sham and Laplace-Beltrami equations are derived. Simulations are implemented based on the coupled governing equations and compared with experimental results.