Micro-electro-mechanical system (MEMS) vapor cells are key components for sensors such as chip-scale atomic clocks (CSACs) and magnetometers (CSAMs). Many approaches have been proposed to fabricate MEMS vapor cells. In this article, we propose a new method to fabricate wafer-level filling of MEMS vapor cells based on chemical reaction and evaporation. The Cs metals are firstly obtained through the chemical reaction between cesium chloride and barium azide in a reservoir baseplate. Then, the Cs metals are evaporated to the preform through the microchannel plate and condensed on the inner glass surface of the preform. Lastly, the MEMS vapor cells are filled with buffer gas, sealed by anodic bonding, and mechanically diced into three dimensions: 5 mm × 5 mm × 1.2 mm, 4 mm × 4 mm × 1.2 mm, and 3 mm × 3 mm × 1.2 mm. The full width at half maximum (FWHM) linewidth of the coherent population trapping (CPT) signal of the MEMS vapor cells is found to be 4.33 kHz. The intrinsic linewidth is about 1638 Hz. Based on the CPT signal, the frequency stability is 4.41 × 10−12@1000 s. The results demonstrate that the presented method of the wafer-level filling of MEMS vapor cells fulfills the requirements of sensors such as CSACs.