A method for manufacturing a composite substrate that prevents undesirable effects of etching a thin film includes a pattern forming step, an ion implanting step, a bonding step, and a separation step. In the pattern forming step, a pattern region and a reverse pattern region are formed on a principal surface of a functional material substrate. In the ion implanting step, by implanting ions into the functional material substrate, a separation layer is formed inside at a certain distance from the surface of each of the pattern region and the reverse pattern region. In the bonding step, the functional material substrate at the pattern region is bonded to a supporting substrate. In the separation step, the pattern region is separated from the functional material substrate, and the reverse pattern region is made to fall off.