The demands for novel approaches that enhance safety and alleviate issue of aging in lithium-ion batteries are increasing and have promoted the development of new battery materials and fabrication techniques. In this study, polymer/ceramic fibers were created by combining the polyimide polymer and polysilsesquioxane (PSSQ) precursors in a one-step gas-assisted electrospinning process and used as separators in lithium-ion batteries. The resultant PI/PSSQ (90:10 wt%) hybrid fiber mats showed excellent thermal dimensional stability at elevated temperature and retained their structural integrity even after being ignited, lowering the risk of battery internal shorting. It was found that PI/PSSQ nanofibrous membranes exhibit higher porosity, superior electrolyte uptake and ionic conductivity in relation to the commercial microporous polyolefin separator (Celgard). As a result of the excellent electrochemical properties, PI/PSSQ separators outperformed Celgard separators by possessing better cyclic stability and rate performance. In addition, PI/PSSQ hybrid separators were elevated under high-voltage condition and also delivered obvious enhancement as compared to Celgard. Therefore, the PI/PSSQ hybrid separator can be regarded as a promising candidate for application in lithium-ion batteries.