The present invention discloses a high-stacked fan-out system level encapsulating structure and a manufacture method thereof. The encapsulating structure comprises: a first encapsulating module, which comprises at least two first encapsulating units stacked in sequence from bottom to top; the first rewiring layers of the adjacent first encapsulating units being electrically connected through the connector in the first module, and at least one of the first rewiring layers of the first encapsulating unit extending to the edge of at least one side of the first encapsulating module; a second encapsulating module, which is located on at least one side of the first encapsulating module, the second rewiring layer of the second encapsulating unit which is adjacent to the first encapsulating module electrically connecting with the first rewiring layer which extends to the edge through an inter-module connector; a flexible circuit substrate, which electrically connects with the first rewiring layer of the first encapsulating unit which is the lowest in the first encapsulating module and the second rewiring layer of the second encapsulating unit in the second encapsulating module respectively through outward connectors. The present invention reduces average distances between the encapsulating structure devices and makes interconnection more freely.