As a derivative of Bi₂Te₃-based compounds, GeBi₂Te₄-based materials have attracted intense attention for thermoelectric applications owing to their low lattice thermal conductivity originating from complex crystal structures and cation disorder. Point defects engineering serves as an effective strategy for optimizing thermoelectric performance of GeBi₂Te₄. However, experimental characterization of point defects and their influence on electrical transport properties still require further investigations. To address this issue, this study successfully fabricated a series of highly crystalline quality GeBi₂Te₄ (000l)-based thin films on Al₂O₃ (000l) substrates using molecular beam epitaxy (MBE) technique. The Bi flux was systematically varied from 0.035 Å/s to 0.075 Å/s to investigate its role in tuning intrinsic point defects and inducing possible phase structure transition. Reflection high-energy electron diffraction (RHEED) and X-ray diffraction (XRD) results demonstrated the high crystalline quality of GeBi₂Te₄ (000l)-based thin films. Scanning tunneling microscope (STM) measurements identified GeBi and TeBi antisite defects as the dominant point defects in GeBi₂Te₄. Angle-resolved photoemission spectroscopy (ARPES) was employed to probe the electronic band structure of GeBi₂Te₄ (000l) films, showing linearly dispersive topological surface states across bulk band gap and Fermi level (EF) positioned inside conduction band. The electron density first increased and then decreased as increasing the Bi flux, which agrees with the shift trend of EF revealed by ARPES, likely due to the synergistic effect of p-type GeBi and n-type TeBi antisite defects. Moreover, when the Bi flux reached 0.075 Å/s, the film phase transitioned from GeBi₂Te₄ to GeBi₄Te₇. The optimized GeBi₄Te₇ thin film exhibited the highest room-temperature carrier mobility of 48.2 cm²V^-1s^-1 among all films, and acquired excellent power factors of 1.3 mWm^-1K^-2 at 300 K and 1.7 mWm^-1K^-2 at 400 K, representing one of the highest values reported for GeBi₂Te₄-based materials. The key findings of this work lay on the direct visualization of intrinsic point defects and the discovery of high performance GeBi₄Te₇ with a high carrier effective mass. These results demonstrate that point defects engineering combined with phase structure regulation are effective for optimizing carrier transport and electrical properties of GeBi₂Te₄-based thin films and bulks.