Spectral analysis and continuous wavelet analysis were conducted on the natural gamma ray logging data from the Middle Miocene-Pliocene Hanjiang, Yuehai and Wanshan formations of well HZ0811 and HZ1811, which locate at northern Huizhou depression and Huilu low uplift at Zhuyi depression, respectively. Significant Milankovitch sedimentary cycles were identified, and “floating” astronomical time scales of well HZ0811 and HZ1811 were established through Gaussian band filtering of short eccentricity signals. The sedimentary rate of Hanjiang-Wanshan formations of well HZ0811 and HZ1811 were calculated according to floating astronomical time scale. The variations of sedimentary rate indicate significant 1.0 Ma and 0.4 Ma cyclicities, which may be related to the sea level change controlled by long eccentricity cycles.