Fluorine resin membranes with excellent chemical resistance have great potential for the application of high-performance chemical protective clothing. However, it is difficult to integrate fluorine resins into other materials such as fabrics due to their lower surface energy and poor bondability, making the fabrication of composite fabrics and the further seal splicing challenging. In this study, atmospheric pressure dielectric barrier discharge (DBD) plasma in helium (He) and helium/acrylic acid (He/AA) mixture atmospheres were used to modify two kinds of fluorine resins, ethylene tetrafluoroethylene (ETFE) and polytetrafluoroethylene (PTFE) membrane. The surface chemical properties, physical morphology, hydrophilicity and adhesion strength of the fluororesin membranes before and after plasma treatments were systematically analyzed. The results showed that the plasma treatment can modify the membrane surface at the nanoscale level without damaging the main body of the membrane. The hydrophilicity of the plasma-treated membrane was improved with the water contact angle decreasing from 95.83° to 49.9° for the ETFE membrane and from 109.9° to 67.8° for the PTFE membrane, respectively. The He plasma creates active sites on the membrane surface as well as etching the membrane surface, increasing the surface roughness. The He/AA plasma treatment introduces two types of polyacrylic acid (PAA)—deposited polyacrylic acid (d-PAA) and grafted polyacrylic acid (g-PAA)—on the membrane surface. Even after ultrasonic washing with acetone, g-PAA still existed stably and, as a result, improved the polarity and adhesion strength of fluororesin membranes. This work provides useful insights into the modification mechanism of DBD plasma on fluorine resins, with implications for developing effective strategies of integrating fluorine resin membrane to chemical protective clothing fabrics.