From the perspective of the instantaneous frequency and amplitude of climatic wave series and by virtue of the technique of least square support vector machine (LS-SVM), a new prediction method of climatic series is proposed based on the separation of amplitude and frequency. A 30-pentad prediction test on Nanjing precipitation is conducted using this method. The results show that, the new prediction method based on the amplitude-frequency separation presents good prediction accuracies on both the amplitudes of all modes and the frequencies of higher frequency modes. The accumulated errors of predicted instantaneous frequencies have highly sensitive impacts on the anomaly correlations of modes. This method can distinctly improve the prediction of higher frequency modes. For the lower frequency modes, the boundary effect of ensemble empirical mode decomposition (EEMD) causes remarkable errors on the calculation of instantaneous frequency, which subsequently leads to inaccurate argument and eventually results in unsatisfactory prediction on modes of lower frequencies. Thereby, implementing both amplitude-frequency separation and LS-SVM for the prediction of higher frequency modes of climatic series while merely using LS-SVM for the prediction of lower frequency modes can give perfect predictions on components of both higher and lower frequencies, and ultimately improve the prediction of the whole climatic series. The test implementing this frequency-based prediction method on prediction of precipitation in Nanjing shows that the anomaly correlation remains greater than 0.4 in its 30-pentad prediction.