A MEMS package structure, including a substrate, an interconnecting structure, an upper metallic layer, a deposition element and a packaging element is provided. The interconnecting structure is disposed on the substrate. The MEMS structure is disposed on the substrate and within a first cavity. The upper metallic layer is disposed above the MEMS structure and the interconnecting structure, so as to form a second cavity located between the upper metallic layer and the interconnecting structure and communicates with the first cavity. The upper metallic layer has at least a first opening located above the interconnecting structure and at least a second opening located above the MEMS structure. Area of the first opening is greater than that of the second opening. The deposition element is disposed above the upper metallic layer to seal the second opening. The packaging element is disposed above the upper metallic layer to seal the first opening.