Wave overtopping is a common natural phenomenon occurring in coastal areas and may damage the bricks on the top of breakwaters. The analysis of the bricks' damage process is conducted by many studies, whilst most of them ignored the influence of the mortar layer under the brick. This study develops a three-dimensional numerical model based on the Smoothed Particle Hydrodynamics (SPH) coupled with Discrete Element Method (DEM) to simulate the interactions between the fluid and multi-bodies. The validation of the numerical model is proved by comparison with the experiments. Subsequently, a mortar layer failure model is proposed based on the available numerical flume, and the effect of this model on the motion of the armour bricks is discussed. Meanwhile, the brick-fluid and brick-brick interactions under wave overtopping are simulated and analysed at different instants. Finally, the damage process of armour bricks on the breakwater caused by wave overtopping is well reproduced. The results indicate that the numerical model developed in this study will facilitate the development of marine disaster prevention and mitigation engineering, particularly in forecasting marine hazards. © The Author(s) under exclusive licence to OWZ 2023.