The bi-millennial Heinrich Stadial 5 (HS 5) event, occurring approximately 48 thousand years ago (kyr BP, before 1950 AD), represents a notable cooling episode during the last glacial period in the Northern Hemisphere. However, our comprehension of its impact on Asian summer monsoon variability remains incomplete, largely because of the scarcity of precisely dated and high-resolution records. Here, we present stalagmite δ18O-inferred absolutely dated decadal-resolved evolution of the East Asian summer monsoon (EASM) during HS 5 from Xianyun Cave, southeastern China. Stalagmite chronology constrains the occurrence of HS 5 from 48.67 ± 0.13 to 46.42 ± 0.10 kyr BP. The Xianyun stalagmite record distinctly reveals the three-phase evolution of the EASM during HS 5. It includes a gradual onset lasting for 0.79 kyr (phase 1) from 48.67 to 47.88 kyr BP, a weak EASM oscillation phase (phase 2) with three centennial-scale intensified monsoon events during 47.88–46.94 kyr BP, followed by a gradual 520-yr recovery phase (phase 3). In phases 1 and 2, the synchronous climatic shifts and resemblance to three notable centennial-scale events observed in both the Xianyun and Greenland ice core records suggest a rapid atmospheric teleconnection between the North Atlantic and EASM regions. During phase 3, the 5-century monsoon recovery registered in the Xianyun record contrasts sharply with the rapid 60-yr rebound in the Greenland ice core record. This disagreement suggests a plausible decoupling between low- and high-latitude climates, probably related to tropical sea surface temperatures variabilities and the distinct responses of the regional Intertropical Convergence Zone to El Niño Southern Oscillation variabilities. Our study highlights the essential role of tropical ocean-atmosphere coupling systems in the termination stages of millennial-scale HS events.