Most of the methods and models applied hydrological time series themselves to carry out research. It is necessary to implement the multi-scale analysis to the modeling of hydrological time series. Wavelet transform and multi-scale entropy can be applied to the analysis of multiscale time series. The above methods are applied to the hydrological time series in this paper. Comparison among hydrological time series complexity analysis of different stations at multiscale is obtained. In addition, the resolution number of wavelet decomposition can be decided using multi-scale entropy. The results illustrate that the benefit of a wavelet transform of a hydrological time series lies in its capacity to highlight details of the signal with time-frequency resolution at different scales. Furthermore, it is worthwhile to note that analyzing hydrological time series using multi-scale entropy analysis can help us detect some hidden characteristics of the original time series. The above results can provide the reference for water resource planning and application.