A method for manufacturing a semiconductor device, including the following steps. A plurality of first vias are formed in a first dielectric layer in a memory cell region and a peripheral region. A surface treatment is performed on the plurality of first vias to form a plurality of sacrificial layers. The plurality of sacrificial layers are removed to form a plurality of recesses. A plurality of protective layers are formed in the plurality of recesses. A memory device is formed on the first dielectric layer in the memory cell region. A second dielectric layer is formed on the memory device and on the first dielectric layer. A plurality of second vias is formed in the second dielectric layer in the memory cell region and the peripheral region to electrically connect the memory device in the memory cell region and the first vias in the peripheral region, respectively.