A package structure having an MEMS element includes: a packaging substrate having first and second wiring layers on two surfaces thereof and a chip embedded therein; a first dielectric layer disposed on the packaging substrate and the chip; a third wiring layer disposed on the first dielectric layer; a second dielectric layer disposed on the first dielectric layer and the third wiring layer and having a recessed portion; a lid disposed in the recessed portion and on the top surface of the second dielectric layer around the periphery of the recessed portion, wherein the portion of the lid on the top surface of the second dielectric layer is formed into a lid frame on which an adhering material is disposed to allow a substrate having an MEMS element to be attached to the packaging substrate with the MEMS element corresponding in position to the recessed portion, thereby providing a package structure of reduced size and costs with better electrical properties.