The governing equations, discretization method, and grid configuration of non-hydrostatic models are summarized based on review of the development of non-hydrostatic models. As the main limitation of non-hydrostatic models is the low computational efficiency, three kinds of approaches to improving the models efficiency are analyzed. Moreover, the main differences in the governing equations and numerical method between the non-hydrostatic and hydrostatic models are examined. The applications of non-hydrostatic models in coastal wave transformation and estuarine baroclinic problem are shown. The performances of non-hydrostatic models in these cases show that the models have advantages in simulating wave transformation, wave-structure interactions, and fresh water-salt water mixing in estuarial areas. Nevertheless, there are still many problems in the computational efficiency, boundary conditions, sallow-water nonlinearity, wave breaking, and practical applications of non-hydrostatic models. Finally, based on these problems, future directions for non-hydrostatic models are presented.