The aim of this investigation was to examine a methane (CH4)/nitrogen (N2) gas mixture plasma for polytetrafluoroethylene (PTFE) membrane surface modification. The photoemission plasma species in the radio frequency CH4/N2 mixture gas plasma polymerization were identified by optical emission spectroscopy (OES). The change of hydrophilicity and surface free energy was monitored by static contact angle measurement. The influences of plasma power and gas mixture on the PTFE membrane surface properties were studied. We observed a significant increase in the surface energy of the PTFE membrane due to CH4/N2 mixture gas plasma treatments. In this investigation, the changes in the surface morphology of the CH4/N2 mixture gas plasma deposited PTFE membranes were determined with confocal laser scanning microscopy (CLSM). The experimental results also show the essential position of chemical species in the interaction between a CH4/N2 mixture gas plasma and a membrane surface, which can be controlled by surface modification to tailor the hydrophilicity of the PTFE membrane.