Vacuum packaging of Micro-electro-mechanical system (MEMS) devices is a hot topic for its advantages of improving performance and reducing power consumption. In this paper, the physics package of a chip scale atomic clock (CSAC), as a typical kind of MEMS device, is performed by vacuum packaging based on a systematic method proposed by us. The whole process, including low outgassing and thermal stable materials selection, prebaking for desorption, getter firing for absorption and solder reflow for vacuum sealing is introduced thoroughly. The thermogravimetric analysis or thermal gravimetric analysis (TGA) is used to analyze the thermal stability and desorption of materials. The leak rate of physics packages is measured to be less than 4 × 10−10 Pa·m3/s by helium leak detection. The residual gas pressure and composition in physics packages are analyzed after vacuum packaging. The results show a high vacuum ~0.1 Pa in the physics package. The frequency stability is improved from 4.68 × 10−11 to 1.07 × 10−11 @40,000 s. The presented method for high vacuum packaging is also applicable to other MEMS devices.