A semiconductor device and a manufacturing method thereof are provided. The semiconductor device includes a substrate, a plurality of isolation structures, a charge storage layer, and a conductive layer. The substrate has a memory region and a logic region. The substrate in the memory region has a plurality of semiconductor fins. The isolation structures are disposed in the substrate to isolate the semiconductor fins. The semiconductor fins are protruded beyond the isolation structures. The charge storage layer covers the semiconductor fins. The conductive layer is disposed across the semiconductor fins and the isolation structures such that the charge storage layer is disposed between the conductive layer and the semiconductor fins.