The invention provides a manufacturing method of a MEMS device, which includes: providing an integrated circuit device including a substrate and an electrical structure on the substrate, the electrical structure includes at least one sensing region and at least one first connection section; providing a structure layer, and forming at least one second connection section on the structure layer; bonding the at least one first connection section and the at least one second connection section; etching the structure layer for forming at least one movable structure, the movable structure being located at a position corresponding to a position of the sensing region, and the movable structure being connected to the at least one first connection section via the at least one second connection section; and thereafter, providing a cap to cover the movable structure and the sensing region, wherein the movable structure is not directly connected to the cap.