This paper reports a surface functional monomer-directing strategy for the highly dense imprinting of 2,4,6-trinitrotoluene (TNT) molecules at the surface of silica nanoparticles. It has been demonstrated that the vinyl functional monomer layer of the silica surface can not only direct the selective occurrence of imprinting polymerization at the surface of silica through the copolymerization of vinyl end groups with functional monomers, but also drive TNT templates into the formed polymer shells through the charge-transfer complexing interactions between TNT and the functional monomer layer. The two basic processes lead to the formation of uniform core-shell TNT-imprinted nanoparticles with a controllable shell thickness and a high density of effective recognition sites. The high capacity and fast kinetics to uptake TNT molecules show that the density of effective imprinted sites in the nanoshells is nearly 5 times that of traditional imprinted particles. A critical value of shell thickness for the maximum rebinding capacity was determined by testing the evolution of rebinding capacity with shell thickness, which provides new insights into the effectiveness of molecular imprinting and the form of imprinted materials. These results reported here not only can find many applications in molecularly imprinting techniques but also can form the basis of a new strategy for preparing various polymer-coating layers on silica support.