The climatic transitions during the Miocene–Pliocene epochs had significant impacts on the worldwide biological diversity and were associated with large turnovers of continental vegetation and fauna. Previous studies have shown that late Miocene cooling and continental aridification which was initiated 7 Ma reversed to warm conditions across the Miocene–Pliocene Boundary ~ 5.3 Ma. Here we present detailed orbital pacing of Asian monsoon deposits to constrain further the global climate change during this period. We produce high-resolution magnetic susceptibility records which reveal that the 1.2 Myr obliquity modulation would have been the main driving factor of the cooling and warming that occurred ~ 7 Ma and 5.3 Ma, respectively. The Tibetan rise and closures of the Panama and Indonesian seaways enhanced the impact of the 405 kyr eccentricity cycles to an oscillatory climatic state while the Northern Hemisphere glaciations were increasing from 4 to 2.5 Ma.