One of the important MESSENGER observations is the formation of flux transfer event (FTE) showers, where tens of FTEs are observed in a short time interval of about 1–2 minutes, at Mercury’s magnetopause. In this paper, we investigate the interactions between the solar wind and Mercury’s magnetosphere using three-dimensional global hybrid simulations. When the interplanetary magnetic field (IMF) is purely southward, we can observe FTE showers at the low-latitude dayside magnetopause, and these FTEs can propagate northward or southward with a speed of about 90 km s−1. When the IMF is purely northward, FTE showers can be produced in both the northward and southward hemispheres of the high-latitude nightside magnetopause, and these FTEs propagate toward the magnetotail with a speed of about 250 km s−1. The typical FTEs have a duration of 1–2 s, and reoccur in 5–6 s. Our simulations provide a good explanation for FTE showers observed by MESSENGER.