The invention provides a semiconductor device and a manufacturing method thereof, and an electronic apparatus. The method comprises the following steps: providing a semiconductor substrate, wherein multiple gate structures are formed on the semiconductor substrate, and each gate structure includes a gate hard mask layer on the top; sequentially depositing a self-aligned contact barrier layer and an interlayer dielectric layer on the semiconductor substrate to cover the gate structures; removing the interlayer dielectric layer and the self-aligned contact barrier layer between the gate structures to form openings used for filling a material constituting self-aligned contact; depositing another gate hard mask layer on the semiconductor substrate to increase the thickness of the gate hard mask layers on the tops of the gate structures; and removing the part, on the semiconductor substrate between the gate structures, of the another gate hard mask layer. According to the invention, while self-aligned contact is formed, the thickness of the gate hard mask layers on the tops of the gate structures is increased, reduction of breakdown voltage between the self-aligned contact and the gate structures is avoided, and the performance of storage devices is improved.