A compound semiconductor substrate having a desired quality is provided.A compound semiconductor substrate has an SiC (silicon carbide) layer, an AlN (aluminum nitride) buffer layer formed on the SiC layer, an Al (aluminum) nitride semiconductor layer formed on the AlN buffer layer, a first GaN (gallium nitride) layer formed on the Al nitride semiconductor layer, a first AlN intermediate layer formed on the first GaN layer in contact with the first GaN layer, and a second GaN layer formed on the first AlN intermediate layer in contact with the first AlN intermediate layer.