Ga2O3is an emerging wide bandgap semiconductor with potential applications in power and RF electronic systems. Previous studies have focused on β-Ga2O3, and theoretical caculations have been made on the two-dimensional electronic gas(2DEG) in β-(AlxGa1-x)2O3/Ga2O3 heterojunction. In this paper, the effect of ε-(AlxGa1-x)2O3 as a potential barrier on the electron transport properties of ε-(AlxGa1-x)2O3/ε-Ga2O3 heterojunction was studied. Firstly, the structure and properties of ε-(AlxGa1-x)2O3/ε-Ga2O3 heterojunction are introduced. The charge density on the polarization surface caused by spontaneous polarization and piezoelectric polarization of ε-(AlxGa1-x)2O3/ε-Ga2O3 heterojunction and the effect of polarization on the concentration of 2DEG were analyzed and calculated. Then, the relationship between ε-(AlxGa1-x)2O3 barrier thickness and alloy disorder scattering, interface roughness scattering and polar optical phonon scattering were analyzed under different Al mole composition. Finally, it is concluded that the interface roughness scattering and polar optical phonon scattering have important effects on the electron transport properties of ε-(AlxGa1-x)2O3/ε-Ga2O3 heterojunction, and the alloy disorder scattering has little effect on the electron transport properties of ε-(AlxGa1-x)2O3/ε-Ga2O3 heterojunction. The electron mobility of 2DEG concentration, alloy disorder scattering, interface roughness scattering and polar optical phonon scattering are determined by the thickness of ε-(AlxGa1-x)2O3 barrier layer and the Al mole composition.