A semiconductor device and a manufacturing method of the same are provided. The semiconductor device includes a substrate, a first dielectric layer, a first conductive layer, and an isolation structure. The substrate has a trench. The first dielectric layer is disposed on the substrate between two neighboring trenches. The first conductive layer is disposed on the first dielectric layer. The isolation structure, including a step zone and a recessed zone, is disposed in the trench, wherein an upper surface of the step zone is higher than an upper surface of the first dielectric layer.