This study investigates the interannual cross‐seasonal association between the winter energetic particle precipitation, which is related to the geomagnetic activity (GA), and the southern annular mode (SAM) in the following summer by employing the ERA5 reanalysis dataset. The results reveal a marked negative correlation between these variables on an interannual timescale. Therefore, we analyse the GA signatures in the southern atmosphere and find that the evolution of SAM to the negative phase driven by GA may be caused by the following two mechanisms: First, for high GA levels, the middle and lower stratospheric polar vortex becomes weaker from October to November, with considerable changes in the stratospheric thermal structure and more anomalous planetary wave upwelling, accompanied by weakening of the circumpolar westerly. Over time, the anomalous signal from the upper layer can be transmitted downward and is conducive to inducing and strengthening the negative SAM in the following summer, which may serve as the stratospheric pathway for the geomagnetic impact on the SAM and Southern Hemisphere (SH) climate. Second, another possible way is that the preceding GA also appreciably regulates negative anomalies in the Ferrel circulation in SH, implying poleward anomalies in the direction of the pressure gradient, which promotes the development and enhancement of the negative phase of the SAM. In addition, easterly quasi‐biennial oscillation conditioning plays a positive role in the response of the southern atmosphere to geomagnetic forcing, thereby strengthening the connection between them.