A novel hierarchically structured and highly hydrophilic poly(vinyl alcohol-co-ethylene)/poly(ethylene terephthalate) nanoporous separator (referred to NFs/PET/NFs) composed of a poly(ethylene terephthalate) (PET) nonwoven sandwiched between two interconnected poly(vinyl alcohol-co-ethylene) (PVA-co-PE) nanofibrous membranes is successfully developed for lithium-ion battery. Systematical investigations including structural characterization, porosity measurement, water contact angle testing, electrolyte uptake, and thermal shrinkage testing demonstrate that the notable feature of this NFs/PET/NFs nanofibrous separator is an electrolyte-philic, highly porous and hierarchically nanoscaled structure, thus resulting in superior electrolyte wettability, lower thermal shrinkage, and higher ion conductivity, in comparison to the commercial Polypropylene (PP) separator. These structural characteristics enable the NFs/PET/NFs separator to offer an excellent cell performance including outstanding C-rate capability, high capacity and excellent cycling performance. This suggests that the NFs/PET/NFs separator is a promising material for practical application in lithium-ion battery due to it low cost production and high performance.