A package structure and its manufacturing method are provided. The package structure includes a substrate with a recess, and a first MEMS chip, a first intermediate chip, a second MEMS chip and a first capping plate sequentially formed on the substrate. The lower surface of the first MEMS chip has a first sensor or a microactuator. The upper surface of the second MEMS chip has a second sensor or a microactuator. The first intermediate chip has a through-substrate via, and includes a signal conversion unit, a logic operation unit, a control unit, or a combination thereof. The package structure includes at least one of the first sensor and the second sensor.