In an endeavour to improve not only the thermal shrinkage but also the electrochemical performance of separators in lithium-ion batteries, a novel composite separator is developed, i.e., a close-packed SiO2/poly(methyl methacrylate) (PMMA) binary nanoparticles-coated polyethylene (PE) separator. The introduction of SiO2 nanoparticles to the coating layer effectively suppresses thermal shrinkage of the composite separator. In contrast to a SiO2/PMMA coating layer having a film-shaped PMMA binder, the SiO2/PMMA binary nanoparticle coating layer employs PMMA particles as a binder. As a consequence, a highly porous structure, i.e., well-connected interstitial voids, is formed between the binary SiO2 and PMMA nanoparticles. The unique porous morphology allows favourable liquid electrolyte wettability and facile ionic conduction, which play a crucial role in improving cell performance such as the discharge capacity and the C-rate capability of the composite separator.