Exploring the seasonal atmospheric processes involved with hydroclimate changes of the East Asian Summer Monsoon (EASM) during the Mystery Interval (MI, 17.5–14.5 ka BP) will enhance understanding of the EASM climate system. Here we report on the δ2H values of leaf wax n-alkanes (δ2Halk) in a wetland core retrieved from southern China. These values are relatively negative during the MI, contrasting to positive excursion recorded by stalagmite δ18O in nearby caves during the same period. Considering the overlap of the primary synthesis time of leaf waxes in deciduous woody plants and periods of precipitation δ2H alteration in the EASM (late spring to early summer), we interpret the relatively negative signal of δ2Halk in the wetland core as the early onset of summer rainfall during the MI. The early onset of summer rainfall was likely due to the early northeastward shifting of the Western Pacific subtropical high due to the low land-sea thermogradient between the Qinghai-Tibet Plateau and the West Pacific Ocean.