The core-shell molecularly imprinted polymers were optimized to provide reliable connections that allow molecularly imprinted polymers to be fixed on SiO2 surface for the efficient separation and purification of beta-estradiol from marine sediment for the first time. To achieve the goal, different preparation methods were used and finally the polymer using 3-methacryloxypropyltrimethoxysilane as coupling agent exhibited the best result, which further confirmed that 3-methacryloxypropyltrimethoxysilane played an indispensable role on improving the inter-particle connections. An offline molecularly imprinted solid-phase extraction with high-performance liquid chromatography method was successfully applied to the isolation and enrichment of beta-estradiol from marine sediment samples with high adsorption capacity, excellent clean-up efficiency, and great enrichment effect as well as high recovery (> 90%) and accuracy (RSD < 8.5%, n = 3). It proved the successful grafting of molecularly imprinted polymers on SiO2 surface and the applicability of the offline molecularly imprinted solid-phase extraction method in the selective extraction and enrichment of beta-estradiol from marine sediment.