The quasi‐biennial oscillation (QBO) impacts the Madden‐Julian Oscillation (MJO) activity with a stronger MJO in QBO easterly (QBOE) than QBO westerly (QBOW) winters. However, this relationship is poorly represented in the current generation climate models. For the first time, this paper applies a stratospheric zonal‐mean nudging in a subseasonal prediction system to capture it. Two strong MJO cases in a QBO‐neutral winter are investigated. The QBO temperature and zonal wind anomalies are added separately as well as together to the stratosphere using nudging in MJO case hindcast. Only by nudging the QBO temperature anomalies while leaving the zonal wind free, can the prediction system capture the observed QBO‐MJO connection. The tropopause instability is found positively correlated to the MJO amplitude, but it cannot fully explain the captured connection. The free‐evolving zonal wind anomalies in the stratosphere due to the nudged QBO temperature are crucial for the captured connection.