The invention discloses a wafer-level vacuum packaging structure and a manufacturing method thereof, and relates to the technical field of micro-electromechanical systems and wafer-level packaging. The wafer-level vacuum packaging structure comprises a first wafer and a second wafer, the first wafer is provided with a hollow cavity, a bonding area is arranged on a lower part of the first wafer, and the first wafer and the second wafer are bonded through the bonding area; a to-be-packaged device is arranged on the second wafer; a vent through hole is formed in the first wafer, and the vent through hole is close to the hollow cavity; and the method is simple, and the vent through hole is formed in the area close to the first wafer, therefore the vacuum in the hollow cavity can reach or approach to the vacuum in a bonding device chamber within a very short time.