A wafer-level system-in-package (WLSiP) packaging method and a WLSiP package structure are provided. The method includes providing a device wafer including a first front surface and a first back surface and providing a plurality of second chips. The method also includes forming an adhesive layer on the first front surface and patterning the adhesive layer to form a plurality of first through-holes. In addition, the method includes bonding the plurality of second chips with a remaining adhesive layer to cover the plurality of first through-holes. Moreover, the method includes forming a plurality of second through-holes, which are connected with the plurality of first through-holes to form a plurality of first conductive through-holes, each first conductive through-hole includes a second through-hole and a first through-hole. Further, the method includes forming a first conductive plug in a first conductive through-hole to electrically connect to one of the plurality of second chips.