A substrate containing a compound semiconductor layer comprises a substrate layer 11, a first semiconductor layer 12 formed on the substrate layer 11, and a second semiconductor layer 13 made of a Group III nitride-based compound semiconductor formed on the first semiconductor layer 12. The semiconductor layer 12 is provided with a plurality of pores 14. Thus, a compound semiconductor layer containing a Group III nitride-based compound semiconductor with excellent surface planarity and crystallinity can be provided, as well as a method for manufacturing the same, and a semiconductor device using the same.