A package structure and a packaging method for manufacturing the package structure are provided. The package structure comprises a cover wafer, a device wafer and a bonding material. The cover wafer has an optical element, and a surface of the cover wafer is defined with a height difference that is greater than 20 micrometers. The bonding material has a width and continuously surrounds the optical device, and is disposed between the cover wafer and the device wafer, in which the width is between 10 micrometers and 150 micrometers. The bonding material hermetically bonds the cover wafer and the device wafer to make a leakage rate of the package structure less than 5e−8 atm-cc/sec.