Abstract Mesoscale convective systems (MCSs) are powerful contributors to extreme precipitation, often resulting in flash floods. However, the extent to which these systems are influenced by natural modes of climate variability is still not fully understood. In this study, we found that the occurrence of extreme precipitation from MCSs nearly doubles during the intense positive phase of the Baroclinic Annular Mode (BAM). The positive phase of BAM slows down the zonal translation speed of extratropical cyclone (ETC) trajectories, creating a favorable dynamical environment for extreme MCS precipitation. Furthermore, we discovered that when ETCs and MCSs coincide, they account for more than 90% of extreme precipitation during springtime in the U.S. These multiscale interactions between the planetary‐scale BAM, synoptic‐scale extratropical cyclones, and MCSs manifest as significant regional impacts on extreme precipitation.