A method for manufacturing a compound semiconductor device includes: providing a semiconductor substrate including a foundation layer having a first conductivity type; forming a deep trench in the foundation layer; and forming a deep layer having a second conductivity type by introducing material gas of the compound semiconductor while introducing dopant gas into an epitaxial growth equipment to cause epitaxial growth of the deep layer in the deep trench. A period in which a temperature in the epitaxial growth equipment is increased to a temperature of the epitaxial growth of the deep layer is defined as a temperature increasing period. In the forming the deep layer, the deep layer is further formed in a bottom corner portion of the deep trench by starting the introducing of the dopant gas during the temperature increasing period and starting the introducing of the material gas after the temperature increasing period.