This paper reported on the microfabrication of alkali metal vapor cells based on the two-step low temperature anodic bonding for the chip-scale integration of atomic clock, atomic magnetometer, atomic gyroscope and other atomic devices. Cell structures were fabricated by Micro-electromechanical System (MEMS) bulk silicon process, and the etched silicon with cells was firstly bonded to Pyrex glass to fabricate preformed chambers by the standard anodic bonding process. Then, nitrogen buffer gas and micro-scale alkali metal (rubidium or cesium) were introduced into the preformed cells. The two-step anodic bonding process was used to seal the cells at a temperature lower than the paraffin flash point (198 ℃). In the first step, bonding voltage was lower than the breakdown voltage of nitrogen buffer gas to pre-seal the cells. In the second step, the bonding was in air atmosphere, and the bonding voltage increased up to 1 200 V to strengthen packaging quality. A high power laser system locally heated the micro-scale alkali metal packets to release alkali metal, and a uniform coating of paraffin was formed on cell walls to prolong the life of the polarized atoms. With proposed method, 95% bonding is achieved by the two-step low temperature anodic bonding, and the alkali rubidium still has a metallic luster after anodic packaging. The achieved minimum volume of double-cells is about 6.5 mm×4.5 mm×2mm. Rubidium absorption spectrum shows that alkali rubidium is effectively encapsulated in the cells. It is feasible to fabricate MEMS alkali metal vapor cells by the two-step low temperature anodic bonding process.