GeBi₂Te₄-based materials have attracted considerable attention for thermoelectric applications due to their low lattice thermal conductivity, which arises from complex crystal structures and cation disorder. Point defect engineering serves as an effective strategy for optimizing the thermoelectric performance of GeBi₂Te₄. However, experimental characterization of point defects and their influence on electrical transport properties still requires further investigation. To address this issue, this study successfully fabricated a series of highly crystalline GeBi₂Te₄ (000l )-based thin films on Al₂O₃ (000l ) substrates using the 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 a possible phase transition. Scanning tunneling microscope (STM) measurements identified Ge_Bi and Te_Bi antisite defects as the dominant point defects in GeBi₂Te₄. Angle-resolved photoemission spectroscopy (ARPES) is employed to probe the electronic band structure of GeBi₂Te₄ (000l) films, revealing linearly dispersive topological surface states across the bulk band gap and a Fermi level (E_F) positioned within the conduction band. The electron density initially increased and subsequently decreased with increasing Bi flux, consistent with the E_F shift trend observed by ARPES-likely due to the synergistic effect of p-type Ge_Bi and n-type Te_Bi antisite defects. Moreover, when the Bi flux reached 0.075 Å/s, the film underwent a phase transition from GeBi₂Te₄ to GeBi₄Te₇. The optimized GeBi₄Te₇ thin film exhibited the highest room-temperature carrier mobility of 48.2 cm²·V^–1·s^–1 among all samples, achieving excellent power factors of 1.3 mW·m^–1·K^–2 at 300 K and 1.7 mW·m^–1·K^–2 at 400 K-among the highest values reported for GeBi₂Te₄-based materials. The key findings of this work lie in 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 defect engineering combined with phase structure regulation is effective for optimizing carrier transport and electrical properties in both GeBi₂Te₄-based materials.