The invention provides an MEMS wafer level vacuum package structure and a manufacturing method thereof. The package structure comprises a silicon cover plate and an MEMS wafer with a movable structure, wherein a vertical through hole is formed on the cover plate, the through hole is internally filled with a conductive material, a bonding surface of the cover plate is provided with a groove, a layer of getter film is arranged at the bottom of the groove, and the silicon cover plate and the MEMS wafer with the movable structure form the vacuum package structure by wafer bonding. The manufacturing method provided by the invention comprises the following steps: at first, manufacturing the through hole on the cover plate, and filling the conductive material in the hole; and then, forming the groove on the bonding surface, depositing a layer of getter film on the bottom of the groove, depositing a layer of multilayer metal film in a bonding area, and wafer bonding the cover plate with the MEMS wafer with the movable structure in a vacuum environment. According to the MEMS wafer level vacuum package structure provided by the invention, the groove with the getter and the through hole are formed on the silicon cover plate to export an electrode from the closed groove without carrying out wire bonding, so that the procedures are simple, meanwhile, the vacuum maintenance ability in the package structure is improved, contamination of granules to the movable structure during cutting is avoided, and performance of the device is guaranteed.