Molecular imprinted composite membranes (MICMs) had attracted much attention in the field of selective separation for bioactive components of natural products. However, it remained a challenge to improve the separation performance of MICMs. Herein, multi-chamber carbon cubes (MCCBs) were synthesized and introduced into polyvinylidene fluoride (PVDF) powders to construct labyrinth structure in molecularly imprinted composite membranes (LMICMs), which were used for efficiently separating acteoside (ACT). The constructed labyrinth structure had complex multidimensional transport routes to trap abundant ACT molecules in LMICMs, thereby improving the rebinding capacities and permselectivity of LMICMs. Meanwhile, the prepared MCCBs with multi-chamber structure can provide a great accommodation space, improving the rebinding capacities of LMICMs. In addition, the labyrinth structure with the large interface resulted in the creation of numerous ACT-imprinted sites and cavities (ACT-ISC) in LMICMs, thus increasing the permselectivity of LMICMs to ACT. Importantly, it was no surprise that large rebinding capacity (154.74 mg/g), excellent rebinding selectivity (4.52) and high permselectivity (14.88) were successfully achieved. It was of great value to design LMICMs with labyrinth structure for efficiently separating of bioactive components from natural products.