The invention relates to a breathable hydrophobic mixed matrix membrane and a preparation method thereof. The method comprises a fluoroalkylation modification method on porous carbon microspheres and a method for preparing the hydrophobic mixed matrix membrane by doping the carbon microspheres into polymers. Micron-size activated carbon powder serves as the porous carbon microspheres, fluoroalkyl chains are grafted on the surface of the porous carbon microspheres sequentially through the processes of strong acid oxidization, fluoroalkylation and the like to obtain fluoroalkylation powder, and then the powder is mixed with the polymers, solvent, an additive and the like to form a membrane preparation solution and prepare the mixed matrix membrane.