Flow over stepped spillway has been studied for centuries, due to its unstable and the characteristics of cavity, the simulation of this type of spillway flow is always difficult. Most of the early studies of flow over stepped spillway are based on experiment, while in the recent decades, numerical studies of flow over stepped spillway draw most of the researchers’ attentions due to its simplicity and efficiency. In this study, a new Lagrangian based particle method is introduced to reproduce the phenomenon of flow over stepped spillway, the inherent advantages of this particle based method provide a convincing free surface and velocity profiles compared with previous experimental data. The capacity of this new method is proved and it is anticipated to be an alternative tool of traditional mesh based method in environmental engineering field such as the simulation of flow over stepped spillway.