The invention discloses a micromolecular high-hydrogen sparkling water and a preparation method thereof, and belongs to the technical field of hydrogen-rich water. The method comprises the following steps: reverse osmosis secondary filtration treatment of water, and electronic ultraviolet disinfection for obtaining purified water; vacuum degassing of the purified water; ultrasonic atomization forobtaining a primary gas-water mixed solution; mixing of the primary gas-water mixed solution and hydrogen in a secondary gas-liquid mixing pump to obtain a secondary gas-water mixed solution; pressurization; and ultrasonic atomization using an aeration head to produce the micromolecular high-hydrogen sparkling water. The concentration of hydrogen in the obtained micromolecular high-hydrogen sparkling water is 6-14 ppm. The primary gas-water mixed solution is prepared in an ultrasonic atomization manner, and the hydrogen and the purified water are fully atomized and mixed to increase the concentration of hydrogen in the final product.