The invention relates to a super-hydrophobic processing method of a polytetrafluoroethylene thin film. The biaxial orientation stretching polytetrafluoroethylene thin film with micro holes is padded into fluorine surfactant mixed liquid and is preheated for 1-10 minutes at 80-150 DEG C and is baked for 1-10 minutes under 110-200 DEG C to prepare the super-hydrophobic polytetrafluoroethylene micro-hole thin film. The super-hydrophobic polytetrafluoroethylene thin film can be widely used in the fields of chemical engineering, energy, environmental protection, medical care, electronic, aviation,protective clothing, etc.