Abstract: Temporal frequency analysis is a good method to research the time-varying non-stationary data.As a typical non-linear hydrological process, groundwater hydrological process shows that its level data is severely non-stationary and has the obvious observation noise. With WA (Wavelet Analysis) and EMD (Empirical Mode Decomposition), it analyzes the shallow groundwater level observation data (1975.1 -2005.12) of Wong village of Bo county in Fuyang city of Anhui province, discovers the groundwater level change period, by the wavelet stochastic simulation, it also puts forward the EMD stochastic simulation, and simulates the groundwater level sequence of test area. The result shows that the EMD is suitable for researching the groundwater level sequence change trend and period.