The invention provides a Ge composite substrate, a substrate epitaxial structure and a preparation method thereof. The preparation method of the Ge composite substrate comprises the following steps: providing a Ge substrate which is provided with an injection surface, wherein the Ge substrate is the Ge substrate with a beveling angle; performing ion injection on the injection surface, thereby forming a defect layer at the preset depth of the Ge substrate; providing a support substrate, and binding the Ge substrate with the support substrate; peeling off partial Ge substrate along the defect layer, thereby transferring partial Ge substrate to the support substrate to form a Ge film on the support substrate, wherein the Ge composite substrate is obtained. By using above mentioned scheme, the problems that the III-V family epitaxial layer is hard to directly grow on the Si-based substrate, the antiphase domain of the III-V family epitaxial layer epitaxially growing on the Ge substrate is hard to inhibit, and the Ge and Si-based material are hard to integrate are solved.