The invention discloses a longitudinal double-cavity atom air chamber and a preparation method thereof. The longitudinal double-cavity atom air chamber is formed by sequentially bonding glass, a silicon wafer and glass, the atomic air chamber comprises an upper-layer air chamber arranged between the upper-layer glass and the silicon wafer, a groove which is communicated with the upper-layer air chamber, etched on the silicon wafer and used for blowing the upper-layer air chamber, a reaction chamber etched on the lower-layer glass, and a filtering channel communicated with the groove and the reaction chamber, wherein the depth of the groove is smaller than the thickness of the silicon wafer, and the filtering channel comprises a first channel etched on the silicon wafer. On the basis of a chemical reaction filling technology, a longitudinal double-air-cavity structure with upper detection and lower reaction is designed, and the size of the occupied space of the air chamber is optimizedthrough the longitudinal structure while the quantitative proportion is reserved; due to the longitudinal structure, impurities generated by gravity limitation can circulate to the upper-layer detection air chamber.