The manipulation of native atomic defects and their thermal excitations plays vital roles in the thermoelectric performance of Mg3Sb2-based materials. While native defects manipulation has been intensively studied in p-type Mg3Sb2, there exists interesting unsolved issue regarding the abnormal semiconducting electrical behavior in most of samples. In this work, high quality Mg3Sb2 and Mg3Bi2 (00l) films are fabricated by molecular beam epitaxy technique, while variable temperature angle-resolved photoemission spectroscopy and scanning tunneling spectroscopy measurements are utilized for resolving the aforementioned issue. The thermal excitation of Mg interstitials (the electron donor) results in an obvious downshift of valence bands with rising temperature in both the p-type Mg3Sb2 and Mg3Bi2. Meanwhile, the interesting temperature-driven Lifshitz transition is discovered in the p-type Mg3Sb2, as indicated by the change of Fermi surface topology. Above the Lifshitz transition temperature, the Fermi level of p-type Mg3Sb2 will enter the bandgap, which leads to the abnormal semiconducting electrical behavior. This work discloses the excitation of native defects and temperature-driven Lifshitz transition, which are the main causes for the anomalies in electrical transport of p-type Mg3Sb2-based materials, and also provides valuable insights for further improving their thermoelectric performance.