Two-dimensional electron gas (2DEG) coexists with topological states on the surface of topological insulators (TIs), while the origin of the 2DEG remains elusive. In this work, electron density in TI thin films (Bi2Se3,Bi2Te3, and their alloys) were manipulated by controlling the density of electronically active native defects with particle irradiation. The measured electron concentration increases with irradiation dose but saturates at different levels for Bi2Se3 and Bi2Te3. The results are in quantitative agreement with the amphoteric defect model, which predicts that electronically active native defects shift the Fermi energy (EF) toward a Fermi stabilization level (EFS) located universally at ̃4.9 eV below the vacuum level. Combined with thickness-dependent data, it is demonstrated that regardless of the bulk doping, the surface EF is always pinned at EFS, producing a band bending and 2DEG on TI film surfaces. Our work elucidates native defect physics of TIs with a model universally applicable to other semiconductors and has critical implications for potential device applications of TIs.