The graphite-resin composite bipolar plates prepared by the traditional hybrid pressing process exhibit poor conductivity, processability, and wettability due to the graphite flake layer being covered by resin, hindering the formation of a continuous conductive network, which significantly constrains their promotion and application in the field of proton exchange membrane fuel cells (PEMFC). In this paper, an ultra-thin flexible graphite/epoxy composite bipolar plates (BPs) with a thickness of only 0.775 mm is prepared followed by a process of flexible graphite preforming and impregnation curing. The hydrophilicity-modified BPs surface has a contact angle of 59.01° as well as flexural and compressive strengths of 11 MPa and 4 MPa and possesses a high in-plane conductivity of 380 S/cm and a low in-plane specific resistance of 6 mΩ cm2. The electrostack test results show that the hydrophilic runner channel is more conducive to the diffusion and spreading of H2O generated from the cathode-side reduction reaction in the flow channel, so that O2 smoothly passes through the gas diffusion layer to participate in the reduction reaction of O2, and exhibits higher electric power at high current density, while the hydrophobically modified BPs has relatively poor overall performance due to ohmic losses.