The ‘Mystery Interval’ (MI, 17.5−14.5 ka) was the first stage of the last deglaciation, a key interval for understanding mechanisms of glacial–interglacial cycles. To elucidate possible causes of the MI, here we present three high-resolution, precisely dated oxygen-isotope records of stalagmites from Qingtian and Hulu Caves in China, reflecting changes in the East Asian summer monsoon (EASM) then. Based on well-established chronologies using precise 230Th dates and annual-band counting results, the two-cave δ18O profiles of ~7-yr resolution match well at decadal timescales. Both of the two-cave records document an abrupt weakening (2‰ of δ18O rise within 20 yr) in the EASM at ~16.1 ka, coinciding with the transition of the two-phased MI reconstructed from New Mexico's Lake Estancia. Our results indicate that the maximum southward displacement of the Intertropical Convergence Zone and associated southward shift of polar jet stream may generate this two-phase feature of the MI during that time. We also discover a linear relationship among decreasing EASM intensity, rising atmospheric CO2 and weakening Atlantic Meridional Overturning Circulation between the MI and Younger Dryas episodes, suggesting a strong coupling of atmospheric/oceanic circulations in response to the millennial-scale forcing, which in turn regulates global climate changes and carbon cycles.