This paper introduced a method of forecasting precipitation with frequency spectrum analysis. With the method, tendency of measured value was analyzed, harmonic mode was checked by using autocorrelation function, the relation between spectrum parameters was analyzed and Fourier coefficient was calculated based on the theory of Fourier series. Finally, the significance of every period was tested and dominant period determined so as to establish the prediction model. The method has been used to forecast the annual precipitation in the Naolihe River Basin, The results show that it has two dominant periods, namely three years and nine to ten years, which reflect the regularity of climate change in the area. The practice indicates that the forecasting effect of spectrum analysis method is very good, which could provide basis for the development and management of water resources in the Naolihe River Basin.