The invention relates to a monodisperse hydrophobic silica defoaming agent for purifying high sulfur natural gas and a preparation method thereof, which belong to the technical field of petrochemical industry. The monodisperse hydrophobic silica defoaming agent for purifying high sulfur natural gas is emulsified through monodisperse hydrophobic silica which are uniform in distribution of particle sizes and are smaller than 5% in deviation and mobile carrier non-polar insoluble oil, the surfaces of particles can be modified by using different hydrophobic agent siloxanes and polydimethyl siloxane fluids, perfectly customize physicochemical property of hydrophobic agents by controlling the amount of the hydrophobic agent, and the monodisperse hydrophobic silica, mobile carriers, emulgators, thickeners and deionized water are emulsified according the quality radio of (0.2-5.0): (10-25): (1-5): (1-5): (60-87.8) at last, thereby enabling defoaming agent particles to obtain excellent defoaming and inhibiting effects.