The invention discloses a method for preparing a protective coating on the surface of a bipolar plate of a fuel cell. The method comprises the following steps: S1, setting a pair of Cr targets and a pair of Ta targets as a target material of a coating chamber, and respectively placing the Ta targets and the Cr target on two ends of a coating device; and S2, putting the substrate material of the bipolar plate of the fuel cell in the coating chamber, carrying out vacuum coating by using a plasma enhanced magnetron sputtering technology and depositing a CrN/TaN superlattice film layer on the surface of the bipolar plate of the fuel cell. Compared with the prior art, the invention has the following advantages: the corrosion resistance of chromium nitride and the hardness and corrosion resistance of tantalum nitride are fully integrated, and the compounded multi-layer film is greatly improved in corrosion resistance, toughness and wear resistance; and the noble metal or amorphous carbon film prepared on the surface can provide excellent electrical conductivity, so the requirements of the metal bipolar plate of the fuel cell for high electrical conductivity, corrosion resistance and long-term use can be met.