316 L stainless steel is an ideal bipolar plate material for a proton exchange membrane fuel cell (PEMFC). However, the thickening of the passivation film on the stainless steel surface and the dissolution of corrosive ions during operation will affect the durability of the PEMFC. Herein, a heterogeneous layer is prepared on the surface of 316 L stainless steel through dual ion implantation of molybdenum ion and carbon ion combined with heat treatment to promote the corrosion resistance and conductivity of the bipolar plate. The ion implantation technique resulted in a uniform distribution of Mo and C elements on the surface of 316 L stainless steel, with a modified layer depth of about 70–80 nm. The electrical conductivity of the ion implanted samples was significantly improved, and the interfacial contact resistance was reduced from 464.25 mΩ × cm² to 42.49 mΩ × cm². Heat treatment enhances the surface homogenization, repairs the defects of irradiation damage, and improves the corrosion resistance of stainless steel. The corrosion current density of (Mo+C)-600 samples decreased from 1.21 × 10⁻⁸ A/cm² to 2.95 × 10⁻⁹ A/cm² under the long-term corrosion condition of 4 h. These results can provide guidance for the modification of stainless steel bipolar plates.