As a Lagrangian mesh-free method, the Moving Particle Semi-implicit (MPS) method is very suitable for simulating violent flows, such as breaking waves on free surface. However, despite its wide range of applicability, the original MPS algorithm suffers from some inherent difficulties in obtaining an accurate fluid pressure in both spatial and time domain. Different modifications to improve the method have been proposed in the literature. In this paper, we propose the following modifications to improve the accuracy of pressure calculations and the stability of the method: (i) A mixed source term in the pressure Poisson equation with no artificial term in the formulation, (ii) New solid and free surface boundary handling methods, (iii) Particle position shifting and collision handling, and (iv) A new version of “cell-link” neighbour particle searching strategy, which reduces about 6.5/9 (∼72%) of the searching area compared with traditional “cell-linked” algorithm.The proposed modifications are verified and validated by some model free-surface flow problems, such as a two-dimensional dam break (with rigid and flexible structures on the impacting end—FSI model), liquid sloshing and ship cross section dropping problems. The numerical results obtained are found to be in good agreement with the available numerical or experimental results. With the proposed modifications, the stability and accuracy of the pressure field are improved in spatial and time domains.