Display omitted •Bonding interface is modified to a homogenous one with an epitaxial layer.•Epitaxial layer constrains the defects, disperses and reduces the heterogenous mismatch stress.•Epitaxial layer is doped to reduce the carrier recombination leakage current in this defect-rich layer. In the realm of optoelectronic integration, silicon-based Ge bonding has attracted great attention due to its advantages in short-wave infrared response and low cost. However, owing to the inherent lattice mismatch and thermal mismatch between Ge and Si, the bonded Ge-Si heterogenous interfaces encountered problems of thermal instability and high interface states. Herein, an approach of separating the bonding interface from the heterogenous interface is proposed through inserting a Ge epitaxial layer (GeEL) between the Si substrate and Ge film. This separation modifies the bonding interface to a homogenous one, alleviating the massive mismatch stress and achieving film relaxation, enhancing bonding stability in all aspects. Moreover, during 850 °C annealing, GeEL is doped via diffusion hence realizes electric filed modulation, inhibiting the carrier recombination leakage current and trap assisted tunneling in this defect-rich layer. A Ge-Si heterogenous PIN diode prepared by this bonding method has achieved a remarkable low dark current density (1.33 mA/cm2), a low ideality factor (1.11), and a high on–off ratio (106), confirming the outstanding quality of the bonded heterojunction. This work provides great prospects for higher performance, larger scale and multi-functional Si-based heterogenous material device applications.