A MEMS microphone packaging method includes the steps of: providing a substrate having a conducting part and a through hole; mounting a processor chip on the substrate and electrically connecting the processor chip to the conducting part; mounting a sensor chip on the substrate over the through hole and adjacent to the processor chip and electrically connecting the sensor chip to the processor chip; and mounting a cover on the substrate over the processor chip and the sensor chip. The cover has a conducting circuit, and the conducting circuit electrically coupled with the conducting part. Thus, the method of the invention can make a flip architecture MEMS microphone, reducing the steps of the packaging process and lowering the degree of difficulty of the manufacturing process and the manufacturing costs.