The surface topography of micro-EDM is closely related to its application range, so it is important to accurately predict the surface morphology. Most of the existing models do not consider the stochastic characteristics and uncertainty of the discharge process, which could produce great differences with the experimental results. Aiming at these problems, the stochastic characteristic of the discharge crater size is studied, and a simulation model is established to predict the surface topography of EDM considering the stochastic characteristics of crater size. Firstly, the stochastic characteristics of the crater size were investigated through the finite-successive pulses discharge method and characterized from the perspective of probability theory. The stochastic characteristics was explained by analyzing discharge waveforms. Secondly, the response surface method (RSM) was used to map the corresponding relationship between the input machining parameters and the distribution characteristics of crater size. It was observed that the RSM model can accurately predict the distribution characteristics of crater size in the range of parameters selected in this study. Finally, models based on stochastic distribution of crater size (MSDS) and fixed crater size (MFS) were established respectively. By analyzing the characteristics of the simulated surfaces and the machined surface, it was found that the surface features of MSDS are closer to the real surface features. Compared with MFS, the roughness prediction error and the average of overall error of MSDS are reduced by 1.01% and 18.97% respectively. The results of this work are helpful to understand the randomness and realize the controllability of EDM.