Based on the analysis of properties of protonic excitation and displacements in the hydrogen bonded molecular systems we proposed here a new model Hamiltonian and theory for studying the properties of nonlinear collective excitation and proton transfer resulting from the localized fluctuation of protons and the deformation of structure of heavy ionic sublattice owing to the protonic displacements.We give the equations of motion and corresponding solutions of solitons,discuss the features and meanings of these solutions and the advantages of our model,and explain completely motion of two kinds of defects and proton transfer in the hydrogen bonded molecular systems.