Safety issues in lithium‐ion batteries (LIBs) have aroused great interest owing to their wide applications, from miniaturized devices to large‐scale storage plants. Separators are a vital component to ensure the safety of LIBs; they prevent direct electric contact between the cathode and anode while allowing ion transport. In this study, the first design is reported for a thermoregulating separator that responds to heat stimuli. The separator with a phase‐change material (PCM) of paraffin wax encapsulated in hollow polyacrylonitrile nanofibers renders a wide range of enthalpy (0–135.3 J g−1), capable of alleviating the internal temperature rise of LIBs in a timely manner. Under abuse conditions, the generated heat in batteries stimulates the melting of the encapsulated PCM, which absorbs large amounts of heat without creating a significant rise in temperature. Experimental simulation of the inner short‐circuit in prototype pouch cells through nail penetration demonstrates that the PCM‐based separator can effectively suppress the temperature rise due to cell failure. Meanwhile, a cell penetrated by a nail promptly cools down to room temperature within 35 s, benefiting from the latent heat‐storage of the unique PCM separator. The present design of separators featuring latent heat‐storage provides effective strategies for overheat protection and enhanced safety of LIBs.