As the core component of controlling the water vapor transmission of proton exchange membrane fuel cell (PEMFC), gas diffusion layer (GDL) has an important influence on the performance of PEMFC.After soaking the carbon paper (CP) with Polytetrafluoroethylene (PTFE) , the carbon paper treated with alternating hydrophilic and hydrophobic pressing by mold filling was obtained, and the hydrophilic and hydrophobic alternating gas diffusion layer (GDL) was prepared by microporous layer (MPL) coating process, in order to improve the water management ability of proton exchange membrane fuel cell (PEMFC). The structure and performance of hydrophilic and hydrophobic alternating GDL at the base layer were characterized by the data of appearance, contact angle, SEM, EDS, through plane (TP) resistivity, through plane (TP) permeability and assembled single cell polarization curve. The results show that the carbon paper impregnated with PTFE formed the striped hydrophilic area and hydrophobic area. The GDL assembled with alternating hydrophilic and hydrophobic treatment had a voltage of 0.47 V and power density of 948 mW/cm2. In the same case, the GDL assembled with undifferential hydrophobic treatment had 0.44 V and power density of 884 mW/cm2. Compared with the GDL assembled with undifferential hydrophobic treatment, the voltage and power density at 2 A/cm2 increased by 6.82% and 7.24%, respectively.