A method for forming a micro-electro-mechanical system (MEMS) device structure is provided. The MEMS device structure includes a micro-electro-mechanical system (MEMS) substrate, and a substrate formed over the MEMS substrate. The substrate includes a semiconductor via through the substrate. The MEMS device structure includes a dielectric layer formed over the substrate and a polymer layer formed on the dielectric layer. The MEMS device structure also includes a conductive layer formed in the dielectric layer and the polymer layer. The conductive layer is electrically connected to the semiconductor via, and the polymer layer is between the conductive layer and the dielectric layer.