As the substrate of a gas diffusion layer (GDL) of a proton exchange membrane fuel cell (PEMFC), a backing layer (BL) is normally a carbon paper treated with an emulsion like a polytetrafluoroethylene (PTFE) solution. In this article, BLs with different PTFE contents and related fuel cells are fabricated, tested and characterized. Results show that a thin film of PTFE is already coated onto the carbon fibers of a BL, which is hydrophobized by the PTFE solution with a minimum concentration of 0.5 wt%. Both the porosity of the BL and the fuel cell performance are increased with the decreased PTFE concentration in the solution, and the best performance is found for the fuel cell with the BL hydrophobized by the PTFE solution with a minimum concentration of 0.5 wt%. Furthermore, schematic models of the pores of BLs are put forward to explain the mechanisms of the interactions between the formation and transportation of the water droplet and fuel cell performance, and then it is concluded that an ideal GDL should have two major characteristics: first, the carbon fibers of a backing layer are just covered with a thin film of PTFE; second, a microporous layer (MPL) penetrates only one or two layers of carbon fibers just for binding each other, and its surface contact angle is as large as possible. Besides, the superior performance of the optimal BL from our lab is also proved by a third-party fuel cell company during a double-blinded operation.