The ubiquitous presence of tetrabromobisphenol A (TBBPA) in aquatic environments has caused severe environmental and public health concerns; it is therefore of great significance to develop effective techniques to remove this compound from contaminated waters. Herein, a TBBPA imprinted membrane was successfully fabricated via incorporating imprinted silica nanoparticles (SiO2NPs). The TBBPA imprinted layer was synthesized on the 3-(methacryloyloxy) propyltrimethoxysilane (KH-570) modified SiO2NPs via surface imprinting. Eluted TBBPA molecularly imprinted nanoparticles (E-TBBPA-MINs) were incorporated onto a polyvinylidene difluoride (PVDF) microfiltration membrane via vacuum-assisted filtration. The obtained E-TBBPA-MINs embedded membrane (E-TBBPA-MIM) showed appreciable permeation selectivity toward the structurally analogous to TBBPA (i.e., 6.74, 5.24 and 6.31 of the permselectivity factors for p-tert-butylphenol (BP), bisphenol A (BPA) and 4,4′-dihydroxybiphenyl (DDBP), respectively), far superior to the non-imprinted membrane (i.e., 1.47, 1.17 and 1.56 for BP, BPA and DDBP, respectively). The permselectivity mechanism of E-TBBPA-MIM could be attributed to the specific chemical adsorption and spatial complementation of TBBPA molecules by the imprinted cavities. The resulting E-TBBPA-MIM exhibited good stability after five adsorption/desorption cycles. The findings of this study validated the feasibility of developing nanoparticles embedded molecularly imprinted membrane for efficient separation and removal of TBBPA from water.