A method for manufacturing a compound semiconductor device includes: providing a semiconductor substrate that includes a foundation layer; forming a deep trench in the foundation layer; and filling the deep trench with a deep layer having a second conductive type and a limiting layer having the first conductive type. In the filling the deep trench, growth of the deep layer from a bottom of the deep trench toward an opening inlet of the deep trench and growth of the limiting layer from a side face of the deep trench are achieved by: dominant epitaxial growth of a second conductive type layer over a first conductive type layer on the bottom of the deep trench; and dominant epitaxial growth of the first conductive type layer over the second conductive type layer on the side face of the deep trench, based on plane orientation dependency of the compound semiconductor during epitaxial growth.