To improve the lithium-ion transport ability and cycle life of lithium-ion batteries, a high-performance polyimide-based lithium-ion battery separator (PI-SO3) was prepared by chemically grafting zwitterion onto the surface of heat-resistant polyimide nanofiber matrix with the assistance of amino-rich polyethyleneimine (PEI). The PI-SO3 not only maintains good dimensional stability (over 200 °C) and flame retardancy, but also ensures the safety of the battery under extreme conditions. Electrochemical experimental results show that PI-SO3 has high ion conductivity (1.99 mS·cm−1), Li+ transference number (0.632), and excellent oxidation potential (5.28 V), which are all higher than those of pure PI separator (1.14 mS·cm−1, 0.444, and 4.56 V, respectively). Meanwhile, LiCoO2/PI-SO3/Li batteries exhibit excellent high-rate performance (139.5 mAh·g−1 at 5C current) and long-term cycle stability (138.9 mAh·g−1 after 100 cycles at 1C current, and 127.9 mAh·g−1 after 100 cycles at 2C current). In addition, the symmetrical battery, Li/PI-SO3/Li, shows stable more than 360 cycles. Compared with batteries using commercial separators, such as Celgard 2325 and pure polyimide matrix, the assembled coin cells with PI-SO3 separators have higher lithium-ion conductivity, Li+ transference number, and diffusion coefficient after grafting zwitterion, showing better rate ability and capacity retention. In this paper, the modification strategy of thermal-resistant separator by grafting zwitterions provides an efficient way to prepare next generation high-performance lithium-ion batteries with good safety.