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Abstract Mercury possesses a miniature yet dynamic magnetosphere driven primarily by magnetic reconnection occurring regularly at the magnetopause and in the magnetotail. Using the newly developed Magnetohydrodynamics with Adaptively Embedded Particle‐in‐Cell (MHD‐AEPIC) model coupled with planetary interior, we have performed a series of global simulations with a range of upstream conditions to study in detail the kinetic signatures, asymmetries, and flux transfer events (FTEs) associated with Mercury's dayside magnetopause reconnection. By treating both ions and electrons kinetically, the embedded PIC model reveals crescent‐shaped phase‐space distributions near reconnection sites, counter‐streaming ion populations in the cusp region, and temperature anisotropies within FTEs. A novel metric and algorithm are developed to automatically identify reconnection X‐lines in our 3D simulations. The spatial distribution of reconnection sites as modeled by the PIC code exhibits notable dawn‐dusk asymmetries, likely due to such kinetic effects as X‐line spreading and Hall effects. Across all simulations, simulated FTEs occur quasi‐periodically every 4–9 s. The properties of simulated FTEs show clear dependencies on the upstream solar wind Alfvénic Mach number (M_A) and the interplanetary magnetic field orientation, consistent with MESSENGER observations and previous Hall‐MHD simulations. FTEs formed in our MHD‐AEPIC model tend to carry a large amount of open flux, contributing ∼3%–36% of the total open flux generated at the dayside. Taken together, our MHD‐AEPIC simulations provide new insights into the kinetic processes associated with Mercury's magnetopause reconnection that should prove useful for interpreting spacecraft observations, such as those from MESSENGER and BepiColombo.