This is the first paper to present a hybrid method coupling an Improved Meshless Local Petrov Galerkin method with Rankine source solution (IMLPG_R) based on the Navier-Stokes (NS) equations, with a finite element method (FEM) based on the fully nonlinear potential flow theory (FNPT) in order to efficiently simulate the violent waves and their interaction with marine structures. The two models are strongly coupled in space and time domains using a moving overlapping zone, wherein the information from both the solvers is exchanged. In the time domain, the Runge-Kutta 2nd order method is nested with a predictor-corrector scheme. In the space domain, numerical techniques including 'Feeding Particles' and two-layer particle interpolation with relaxation coefficients are introduced to achieve the robust coupling of the two models. The properties and behaviours of the new hybrid model are tested by modelling a regular wave, solitary wave and Cnoidal wave including breaking and overtopping. It is validated by comparing the results of the method with analytical solutions, results from other methods and experimental data. The paper demonstrates that the method can produce satisfactory results but uses much less computational time compared with a method based on the full NS model. © 2014 Elsevier Inc.