A package structure having an MEMS element includes: a chip having at least an MEMS element and a plurality of first conductive pads; a lid disposed on the chip to cover the MEMS element and having a plurality of second conductive pads formed thereon; a plurality of bonding wires electrically connecting the first and second conductive pads; a plurality of first bumps disposed on the second conductive pads, respectively; an encapsulant formed on the chip to encapsulate the lid, the bonding wires, the first and second conductive pads and the first bumps while exposing the top surfaces of the first bumps; and a plurality of circuits formed on the encapsulant and electrically connecting to the exposed first bumps, thereby avoiding the conventional drawback of electrical connection failure caused by position deviation of bonding wires due to mold flow of the encapsulant.