Embodiments of a semiconductor device structure are provided. The semiconductor device structure includes a cap structure. The cap structure includes: a first bonding layer and a cap substrate, and the first bonding layer is embedded in the cap substrate. The semiconductor device structure also includes a substrate structure. The substrate structure includes a substrate and a second bonding layer formed on the substrate. The substrate includes a micro-electro-mechanical system (MEMS) substrate or a semiconductor substrate. The cap structure is bonded to the substrate structure by bonding the first bonding layer and the second bonding layer.