A method for filling wafer-based chip-scale atomic clock absorption cells with a high-purity alkali metal comprising at least one of rubidium and cesium, wherein the method comprises: using an MEMS ICP etching technique to carve a shallow microgroove on the first side of a polished double-sided silicon wafer, to carve an array of absorption cell cavities within the scope of said microgroove, to carve a placement cavity within said scope of said microgroove at the center of said polished double-sided silicon wafer, wherein said absorption cell cavities and said placement cavity have a through hole structure running through both sides of said polished double-sided silicon wafer; bonding the second side of the polished double-sided silicon wafer with a first sheet glass through a glass-silicon wafer level anodic bonding process, putting a precomputed amount of an alkali metal compound into the placement cavity, and bonding the first side of the polished double-sided silicon wafer with a second sheet glass through a glass-silicon wafer level anodic bonding process, so that the shallow microgroove and said second sheet glass define a temporary flow channel for an alkali metal vapour; controlling the intensity of a decomposition reaction of the alkali metal compound by separately adjusting the temperature of the placement cavity to decompose the alkali metal compound and to produce a needed amount of the alkali metal, and vaporizing the alkali metal to produce said alkali metal vapour; diffusing the alkali metal vapour through the temporary flow channel, and cooling the absorption cavities to condense the alkali metal vapour in the absorption cavities; and re-bonding the first side of the polished double-sided silicon wafer with the first glass sheet with glass-silicon wafer level anodic bonding while applying an electrostatic force to make said first glass sheet bending under the influence of said force, in such a way that the temporary flow channel is eliminated so that the absorption cells are sealed at the same time. using an MEMS ICP etching technique to carve a shallow microgroove on the first side of a polished double-sided silicon wafer, to carve an array of absorption cell cavities within the scope of said microgroove, to carve a placement cavity within said scope of said microgroove at the center of said polished double-sided silicon wafer, wherein said absorption cell cavities and said placement cavity have a through hole structure running through both sides of said polished double-sided silicon wafer; bonding the second side of the polished double-sided silicon wafer with a first sheet glass through a glass-silicon wafer level anodic bonding process, putting a precomputed amount of an alkali metal compound into the placement cavity, and bonding the first side of the polished double-sided silicon wafer with a second sheet glass through a glass-silicon wafer level anodic bonding process, so that the shallow microgroove and said second sheet glass define a temporary flow channel for an alkali metal vapour; controlling the intensity of a decomposition reaction of the alkali metal compound by separately adjusting the temperature of the placement cavity to decompose the alkali metal compound and to produce a needed amount of the alkali metal, and vaporizing the alkali metal to produce said alkali metal vapour; diffusing the alkali metal vapour through the temporary flow channel, and cooling the absorption cavities to condense the alkali metal vapour in the absorption cavities; and re-bonding the first side of the polished double-sided silicon wafer with the first glass sheet with glass-silicon wafer level anodic bonding while applying an electrostatic force to make said first glass sheet bending under the influence of said force, in such a way that the temporary flow channel is eliminated so that the absorption cells are sealed at the same time.