The interface layer has great significance on the potential barrier height of the CdTe/GaAs heterointerface. In this study, the electronic properties of the CdTe/GaAs heterostructure prepared by molecular beam epitaxy was investigated in situ by synchrotron radiation photoemission spectroscopy for CdTe thicknesses ranging from 3.5 to 74.6 Å. During CdTe deposition, an As-Te and Ga-Te interface reaction occurred, which caused the out diffusion of Ga. As a result a stable GaTe interface dipole layer (more than 30 Å) was formed, which reduced the potential barrier height by 0.38 eV. The potential barrier height was in proportion to the chemical bonding density and thickness of the Ga-Te interface layer. These results provide a more fundamental understanding of the influencing mechanism of the interface layer on the potential barrier height of the CdTe/GaAs heterointerface.