Polyaniline/polyimide (PANI/PI) composites with hierarchical 3D micro/nano-architecture have been prepared via electrospinning and in-situ polymerization. The PANI/PI composite prepared from 0.2 M aniline (PANI/PI-2) exhibited a small average pore size (1.730 μm) and a narrow pore size distribution (1.552–1.882 μm). Compared to the commercial polyolefin separators, the PANI/PI composite separator possesses a much better thermal stability up to 180 °C, a higher porosity (84%), a larger liquid electrolyte uptake (619%) and a higher ionic conductivity (2.33 mS cm−1). The cell with PANI/PI-2 composite separator showed a low interfacial resistance, an enhanced capacity (133 mAh g−1 at 0.2C), a better rate capability (41.4% at 10C) and cyclability (89.3% retention after 500 charge/discharge cycles at 0.2C). The PANI/PI composite with a superior thermal stability and high electrochemical performances is a promising candidate for uses in high perform LIBs.