Spectrogram analysis of seven natural gamma-ray logging of Member 1 of the Qingshankou Formation (K2qn1) and Member 1 and 2 of the Nenjiang Formation (K2n1-2) of Late Cretaceous age in the Songliao Basin reveals sedimentary cyclicities controlled by Milankovitch climate periodicities. The recognition of Milankovitch cycles allows estimation of an average accumulation rate of ~7.55–8.62 cm/ka for the K2qn1 sections, and ~6.69–10.16 cm/ka for the K2n1-2 sections. Two marine transgression events occurred during the deposition of K2qn1 and K2n1-2 and their ages are at ~0.74–1.10 Ma and ~2.38–4.84 Ma, respectively. Identification of Milankovitch cycles from fine-grained deep lake sedimentary rocks in the Songliao Basin may provide great potential for high-resolution stratigraphic subdivisions and correlations.