In this study, a novel boehmite (AlOOH) nanowhiskers/polyethylene (PE) separator was initially prepared by the AlOOH nanowhiskers coating on the commercial PE separator using dip-coating method, in which the AlOOH nanowhiskers were directly synthetized by a facile hydrothermal method. It is shown that the needle-like AlOOH nanowhiskers with the rough surfaces have been successfully obtained. Meanwhile, according to the performance characterization of separators, the AlOOH nanowhiskers/PE separator exhibits higher porosities of 60.1% and excellent mechanical properties with the tensile strength of 145.1 MPa and the elongation of 130.1%, owing to the integrally three-dimensional (3D) structure of AlOOH nanowhiskers coating layer. Also, benefiting from the spindly and rough surficial morphology of AlOOH nanowhiskers, the PE separator coating with AlOOH nanowhiskers has a smaller contact angle of 8.6° and higher electrolyte uptake of 173.1% than that coating with AlOOH nanoparticles. As expected, the LiFePO4/Li cell with AlOOH nanowhiskers/PE separator presents superior cycle stability and rate capacity. Then the SEM images of the lithium metal anode, disassembled from the cell with AlOOH nanowhiskers/PE separator after 200 cycles, show that the 3D structure of AlOOH nanowhiskers layer can suppress the growth of lithium dendrites.