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Microflares, one of small-scale solar activities, are believed to be caused by magnetic reconnection. Nevertheless, their three-dimensional (3D) magnetic structures, thermodynamic structures, and physical links to the reconnection have been unclear. In this Letter, based on high-resolution 3D radiative magnetohydrodynamic simulation of the quiet Sun spanning from the upper convection zone to the corona, we investigate 3D magnetic and thermodynamic structures of three homologous microflares. It is found that they originate from localized hot plasma embedded in the chromospheric environment at the height of 2--10 Mm above the photosphere and last for 3--10 minutes with released magnetic energy in the range of $10^{27}-10^{28}$ erg. The heated plasma is almost co-spatial with the regions where the heating rate per particle is maximal. The 3D velocity field reveals a pair of converging flows with velocities of tens of km s$^{-1}$ toward and outflows with velocities of about 100 km s$^{-1}$ moving away from the hot plasma. These features support that magnetic reconnection plays a critical role in heating the localized chromospheric plasma to coronal temperature, giving rise to observed microflares. The magnetic topology analysis further discloses that the reconnection region is located near quasi-separators where both current density and squashing factors are maximal although the specific topology may vary from tether-cutting to fan-spine-like structure.