Molecularly imprinted membranes (MIMs) have been considered as a promising material for the treatment of intractable micropollutants due to their predetermined selectivity and high stability. Herein, we proposed an exclusive design by incorporation of heterogeneous porous UiO-66-NH2 and hierarchically porous structure nanofibrous membranes to fabricate a MOFs based hierarchically porous molecularly imprinted nanofiber membranes (HP-MINMs) with multiple mass transfer channels, achieving efficient selective removal of atrazine (ATZ). The heterogeneous pores UiO-66-NH2 nanoparticles as matrix facilitated loaded with more densely and accessible imprinted recognition sites. Meanwhile, the multiple transfer channels formed in well-designed hierarchically porous nanofibrous membranes significantly enhancing of permeation flux and increase the contacting efficiency of target molecules with selective recognition sites. As a result, the obtained HP-MINMs possess synchronous enhanced permeation flux (J = 0.40 × 10−3, 1.01 × 10−3 and 1.07 × 10−3 mg min −1 cm −2) and permselectivity factors (β = 3.22 and 3.52), which much superior to those pure molecularly imprinted nanofiber membranes and other references. Importantly, the impressive selective separation performance (the separation efficiency for ATZ is 60.7 %) was achieved in continuous separation process. The presented work provides a fresh idea for addressing the trade-off effect in selective separation of MIMs.