A semiconductor device and a manufacturing method thereof are provided. The semiconductor device includes a first stacked structure, a second stacked structure, an isolation layer and a gate. The first stacked structure is disposed on a substrate, and includes a first GaN channel layer disposed on the substrate and having an N crystal phase and a first barrier layer disposed on the first GaN channel layer. The second stacked structure is disposed on the substrate, and includes a second GaN channel layer disposed on the substrate and having a Ga crystal phase and a second barrier layer disposed on the second GaN channel layer. The isolation layer is disposed between the first stacked structure and the second stacked structure. The gate is disposed on the first stacked structure, the isolation layer and the second stacked structure.