In this study, a novel composite separator based on polytetrafluoroethylene (PTFE) coating layers and a commercial polyethylene (PE) separator is developed for high performance Li-ion batteries. This composite separator is prepared by immersing a PE separator directly into a commercial PTFE suspension to obtain a self-binding PTFE/PE/PTFE tri-layered structure. Then, the as-prepared composite separator is further treated with a H2O2/H2SO4 solution to enhance its electrolyte affinity. The results show that the coating layer, consisting of close-packed PTFE particles, possesses a highly ordered nano-porous structure and an excellent electrolyte wettability property, which significantly enhance the ionic conductivity of the composite separator. Due to the presence of the PTFE-based coating layer, the composite separator exhibits better thermal stability compared with the PE separator, reaching the thermal-resistant grade of commercial ceramic-coated separators. By using different separators, CR2032-type unit half-cells composed of a Li anode and a LiFePO4 cathode were assembled, and their C-rate and cycling performances were evaluated. The cell assembled with the composite separator was proven to have better C-rate capability and cycling capacity retention than the cell with the polyethylene separator. It is expected that the composite separator can be a potential candidate as a coating-type separator for high-performance rechargeable Li-ion batteries.