A method of manufacturing a thin film device includes forming a pair of multi-layered structures by bonding a transfer layer including a thin film device to a temporary transfer substrate, respectively adhering the transfer layers of a pair of the multi-layered structures to both surfaces of a transfer-target substrate; and separating the temporary transfer substrate from each of the transfer layers adhered to the transfer-target substrate. The bonding step includes forming the transfer layer on a transfer-source substrate via a first separation layer separated in accordance with application of a predetermined amount of energy, bonding the transfer layer to the temporary transfer substrate, and separating the transfer-source substrate from the transfer layer by applying energy to the first separation layer to cause a boundary separation and/or an intra-layer separation in the first separation layer.