This paper reports the molecularly imprinted layer-coated silica nanoparticles toward highly selective separation of active diosgenin (DG) from the crude extracts of Dioscorea nipponica Makino (DNM). It has been demonstrated that DG templates were efficiently imprinted into the silica layer by the use of thermally cleavable urethane bonds between DG and 3-isocyanatopropyltriethoxysilane (IPTS), which was synchronously coated onto the surface of silica mother nanoparticles through a seed-directing surface condensation reaction between DG-IPTS and tetraethoxysilicane (TEOS). After removal of templates by simple thermal cleavage reaction, a high density of recognition sites of DG were created in the silica-coating layer. Afterwards, the DG-imprinted silica nanoparticles were evaluated by rebinding experiments and showed a higher selectivity and affinity to DG than commercial silica. When the imprinted particles were used as solid-phase extraction (SPE) sorbents, the recovery yield of DG was up to 90% by one-step extraction from the hydrolysate of DNM, and the purity of DG was larger than 98% by HPLC analysis. These results reported herein provide the possibility for the highly selective separation and purification of active DG from DNM by the molecular imprinting modification at the surface of common silica adsorbents.