A method for integrating a system on an isolation layer. A first isolation substrate including a first circuit deposition region and a first substrate-combining region, and a second isolation substrate including a second circuit deposition region and a second substrate-combining region are provided. Next, a first circuit and a second circuit are respectively formed on the first circuit deposition region and the second circuit deposition region. Next, substrate-connecting elements are formed to connect the first substrate-combining region to the second substrate-combining region. Finally, electrical connecting elements are formed to electrically connect the first circuit and the second circuit.