ZnGeP₂ (ZGP) crystals have attracted tremendous attention for their applications as frequency conversion devices. Nevertheless, the existence of native point defects, including at the surface and in the bulk, lowers their laser-induced damage threshold by increasing their absorption and forming starting points of the damage, limiting their applications. Here, native point defects in a ZGP crystal are fully studied by the combination of high angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and optical measurements. The atomic structures of the native point defects of the Zn vacancy, P vacancy, and Ge-Zn antisite were directly obtained through an HAADF-STEM, and proved by photoluminescence (PL) spectra at 77 K. The carrier dynamics of these defects are further studied by ultrafast pump-probe spectroscopy, and the decay lifetimes of 180.49, 346.73, and 322.82 ps are attributed to the donor V_p⁺ → valence band maximum (VBM) recombination, donor Ge_Zn⁺ → VBM recombination, and donor–acceptor pair recombination of V_p⁺ → V_Zn^-, respectively, which further confirms the assignment of the electron transitions. The diagrams for the energy bands and excited electron dynamics are established based on these ultrahigh spatial and temporal results. Our work is helpful for understanding the interaction mechanism between a ZGP crystal and ultrafast laser, doing good to the ZGP crystal growth and device fabrication.