A waterproof MEMS chip package structure includes a substrate having aa through hole cut through opposing top and bottom surface thereof, a waterproof membrane disposed in the through hole, an along chip bonded to the top surface of the substrate, a MEMS chip stacked on the analog chip and electrically connected to the substrate and the analog chip by wire bonding, and a top cover mounted on the substrate to form an accommodation chamber that accommodates the analog chip and the MEMS chip and communicates with the outside through the through hole. Therefore, the MEMS chip package structure of the present invention utilizes the waterproof membrane to block water vapor from entering the accommodation chamber through the through hole, thereby achieving the effect of protecting the chips.