Background: Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection pressures (such as food shortage and habitat loss) and went through population declines. However, during the mild interglacial periods, many species re-flourished. These temporal dynamics of effective population sizes (N) provide essential information for understanding and predicting evolutionary outcomes during historical and ongoing global climate changes. Results: Using high-quality genome assemblies and corresponding sequencing data, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) method to quantify N changes of twelve representative teleost species from approximately 10 million years ago (mya) to 10 thousand years ago (kya). These results revealed multiple rounds of population contraction and expansion in most of the examined teleost species during the Neogene and the Quaternary periods. We observed that 83% (10/12) of the examined teleosts had experienced a drastic decline in N before the last glacial period (LGP, 110–12 kya), slightly earlier than the reported pattern of N changes in 38 avian species. In comparison with the peaks, almost all of the examined teleosts maintained long-term lower N values during the last few million years. This is consistent with increasingly dramatic glaciation during this period. Conclusion: In summary, these findings provide a more comprehensive understanding of the historical N changes in teleosts. Results presented here could lead to the development of appropriate strategies to protect species in light of ongoing global climate changes.