According to a composite substrate manufacturing method of the present invention, (a) a piezoelectric substrate having minute asperities formed in a rear surface thereof, and a support substrate having a smaller thermal expansion coefficient than the piezoelectric substrate are prepared, (b) a filler is applied to the rear surface 11a to fill the minute asperities, thereby forming a filling layer, (c) a surface of the filling layer is mirror-polished to such an extent that an arithmetic mean roughness Ra of the surface of the filling layer is smaller than an arithmetic mean roughness Ra of the rear surface 11a in a state of above (a), and (d) the surface of the filling layer and a surface of the support substrate are bonded to each other with an adhesive layer interposed therebetween, thereby forming a composite substrate.