How boreal summer intraseasonal oscillation (BSISO) modulates the probability and spatial distributions of extreme occurrence over southeastern China was examined using the real-time BSISO indices and high-resolution gauge-based rainfall and temperature datasets. Strong rainfall variability with a spectral peak at periods of 10–60 days was observed in southern China. The probability density function of rainfall in southern China is skewed toward large values in phases 2–4 of the first component (BSISO1) and in phases 5–7 of the second component of BSISO (BSISO2) life cycle, during which the probability of extreme rainfall events at the 75th (90th) percentile increases by 30–50% (over 60%) relative to the non-BSISO period. Moisture budget indicates that the favorable environment for rainfall extreme is associated with southwesterly moisture convergence over southern China, while the moisture advection contributes insignificantly. High probability of heat wave occurrence are found in densely populated regions over central India (CI), Yangtze River valley (YR) in China, Japan (JP) and Korean Peninsula (KP). A significant increase in HW occurrence in CI (YR) is observed during phases 2–3 (8–1) of the BSISO2 when the 10–30-day anticyclonic and descending anomalies induce enhanced upward thermal heating and sensible heat flux (warm advection) around CI (YR) areas. The northeastward propagating BSISO1 is closely connected to the increased HW probability in JP and KP. During phases 7–8 of the BSISO1, the 30–60-day subsidence along with the low-level anticyclonic anomaly moves into the Northeast Asia sector, leading to enhanced diabatic (adiabatic) warming near surface in JP (KP).