The invention discloses a method for preparing a multifunctional nanometer protective coating through high-duty-cycle pulse discharge, and belongs to the technical field of plasmas. In the method, the interior of a reaction chamber is vacuumized until a vacuum degree is 10-200 millitorrs, inert gas He or Ar is charged, a movement mechanism is started to enable a base material to move in the reaction chamber, monomer steam is charged into the reaction chamber, plasma discharge is carried out, chemical vapor deposition is carried out, a deposition process comprises a pretreatment phase and a film-coating phase, a plasma discharge manner in the pretreatment phase is high-power continuous discharge, and a plasma discharge manner in the film-coating phase is the high-duty-cycle pulse discharge. During a preparation process for the coating, the movement characteristic of the base material and the high-duty-cycle pulse discharge energy of plasmas form combined linkage. The base material moves during the plasma discharge, so that the deposition efficiency of the coating is increased, and the thickness uniformity and compactness of the coating are improved. The prepared coating has the characteristics of being waterproof and moistureproof, mouldproof, resistant to acidic and basic solvents, resistant to acidic and basic salt mist, and the like.