A method for manufacturing the compound semiconductor substrate having a reduced dislocation density at an interface between a Si substrate. Contaminants, such as organic matter and metal, on a surface of a Si substrate are removed whereby a flat oxide film is formed. The oxide film on the surface is removed by using an aqueous hydrogen fluoride solution, whereby hydrogen termination treatment is performed. Immediately after being subjected to the hydrogen termination treatment the temperature of the Si substrate is raised in a vacuum apparatus. If the substrate temperature is raised without any operation, the termination hydrogen is released. Before the hydrogen is released, pre-irradiation with As is performed. Thus, an interface between the Si substrate and the compound semiconductor layer is prepared. Several minutes later, irradiation with Ga and As is performed. Thereby, the compound semiconductor is formed.