The impact of the boreal summer intraseasonal oscillation (BSISO) on rainfall anomalies in the Yangtze–Huaihe River Basin (YHRB) was found to be modulated by the stratospheric quasi‐biennial oscillation (QBO), which is reasonable for the close associations between the QBO and summer extreme precipitation in the YHRB. It was found that the extreme precipitation preferentially occurred in the YHRB during the easterly phase of the QBO (EQBO) compared to the westerly phase of the QBO (WQBO). This was primarily because the BSISO was more prone to cause rainfall extremes in the YHRB during the EQBO summers than during the WQBO summers. The EQBO can induce the background stratospheric easterly wind to arch downward into the troposphere, which enhanced the BSISO‐associated moisture transport and moisture convergence and thus resulted in stronger rainfall extremes in the YHRB.