Disclosed are a GaN-based compound power semiconductor device and a manufacturing method thereof, in which on a GaN power semiconductor element, a contact pad is formed for flip-chip bonding, and a bonding pad of a module substrate to be mounted with the GaN power semiconductor element is formed with a bump so as to modularize an individual semiconductor element. In the disclosed GaN-based compound power semiconductor device, an AlGaN HEMT element is flip-chip bonded to the substrate, so that heat generated from the element can be efficiently radiated.