Numerical attenuation problem is common in constructing vessel’s seakeeping numerical wave tank, which is especially evident in short wave’s simulation. In this article, causes of wave’s attenuation in numerical simulation are analyzed, and the factors affecting the attenuation are got, which are grid size, grid aspect ratio, time step, discretization scheme and free surface reconstruction method. Through a series of comparison simulations, with wave generated by wave boundary method and free surface captured by Volume of Fluid (VOF) method, the quantitative relationship between the impact factors and numerical attenuation is summarized and an optimized setup is got. Using this setup, three short waves are simulated, and the simulation results show good agreement with the theoretical solution.