The separator is a crucial component of lithium-ion batteries, playing a vital role in ion transfer and preventing polarization of the battery. To solve the problem of poor thermal safety of separators in lithium-ion batteries, in this work, three types of hydrophobic silica aerogels are compared. A suitable separator is fabricated by adding hydrophobic silica aerogels with monomethylsilyl as a modifier to pure polyimide. The aerogel composite separator displays a highly cross-linked three-dimensional nanoporous network, a low thermal shrinkage rate (<4 % at 200 °C), and high thermal stability (peak temperature of 670 °C) and oxygen index (>45 %). In addition, owing to the introduced hydrophobic functional groups of Si–CH3, the prepared separator decreases the polarization of the lithium-ion batteries and leads to improved power performance and cycle stability (its discharge voltage difference is 0.42 V higher than that of Celgard 2325 at 5 C). This work provides a new method of improving the safety and simultaneously reducing the polarization of lithium-ion batteries, which has promising application potential in power batteries.