A sustainable, heat-resistant and flame-retardant cellulose-based composite nonwoven has been successfully fabricated and explored its potential application for promising separator of high-performance lithium ion battery. It was demonstrated that this flame-retardant cellulose-based composite separator possessed good flame retardancy, superior heat tolerance and proper mechanical strength. As compared to the commercialized polypropylene (PP) separator, such composite separator presented improved electrolyte uptake, better interface stability and enhanced ionic conductivity. In addition, the lithium cobalt oxide (LiCoO2)/graphite cell using this composite separator exhibited better rate capability and cycling retention than that for PP separator owing to its facile ion transport and excellent interfacial compatibility. Furthermore, the lithium iron phosphate (LiFePO4)/lithium cell with such composite separator delivered stable cycling performance and thermal dimensional stability even at an elevated temperature of 120°C. All these fascinating characteristics would boost the application of this composite separator for high-performance lithium ion battery.