Commercial polyolefin separators with poor electrolyte wettability and inferior thermal stability have hampered the development of advanced lithium-ion batteries (LIBs) due to their unsatisfied electrochemical performance and severe safety hazards. Herein, a novel paper-based composite separator composed of electrolyte-affinitive cellulose fibers (CFs) and thermally stable aramid nanofibers (ANFs) was successfully fabricated through the traditional papermaking method. It was found that the incorporation of ANFs played crucial roles in improving the defects of pure CF separator such as large-sized pores, low mechanical strength and high flammability. Specifically, the CF/ANF composite separator with 20 wt.% ANFs (CF/ANF-20) possessed narrow micropores, satisfied tensile strength (33MPa), excellent thermal resistance (without dimensional shrinkage up to 200 °C) and flame retardancy, greatly enhancing the safe operation of battery. In addition, benefiting from the highly porous structure and exceptional electrolyte affinity of CF separator, the CF/ANF-20 composite separator exhibited appropriate porosity and superior electrolyte wettability, which brought about a high electrolyte uptake (157%), thus endowing it with better ionic conductivity (0.75 mS cm−1) and lower interfacial resistance than that of commercial polypropylene (PP) separator. Accordingly, the LiFePO4/Li half cells using CF/ANF-20 separator delivered outstanding rate capability and stable cycling performance. All results indicate that the CF/ANF-20 separator with great balance between the electrochemical performance and safety is an intriguing candidate for advanced LIBs.