Since nanoparticle imprinted polymer (NIP) can recognize specific nanoparticles which possess complementary chemical and geometrical properties, there are more and more researches dedicated to NIPs for their advantages of lower production cost and higher mechanical strength. To enhance the selectivity and specific adsorption ratio of nanoparticles onto NIPs, numerous experiments were performed to identify the appropriate species as well as the relative ratios of the functional monomers, cross-linkers, and solvents. In addition, the adsorption efficiency of nanoparticles can be improved since nanoparticles tend to self-assemble with patterned NIPs due to the depletion force induced by non-adsorbing polymers. To investigate the effects of dispersant concentration and geometrical complementarity between nanoparticle and NIP, dissipative particle dynamics (DPD) simulations are employed to study the depletion-induced self-assembled behavior between targeted nanoparticle/NIPs systems. It is found that the attraction interaction strength between a nanoparticle and a substrate is larger as the substrate is with complementary cavities, rather than the substrate with patches possessing affinity binding sites. Also, it is observed that the geometric compatibility between the nanoparticles and the substrate pattern is a crucial factor affecting the self-assembly between nanoparticles and NIP substrates. The degree of targets/NIPs association increases as the geometric compatibility grows due to the significant increase in the release of the excluded volume. Moreover, the association efficiency is enhanced as the dispersant concentration rises. The depletion force and association energy of the nanoparticle/NIP systems are calculated for various geometrical conditions. It is found that the degree of association between nanoparticles and substrates increases as the association binding energy grows. Furthermore, the combination effect of the depletion attraction and binding site affinity can augment the association ratio of the systems. A two-dimensional potential profile of a substrate-target pair demonstrate that the nanoparticle tends to follow certain paths with low potential barriers to dissociate. The consequence can be helpful in studying the kinetic behaviors of nanoparticle/NIP systems. These simulation results are important in the signal enhancement of sensor applications and separation efficiency improvement of chromatography and solid extraction treatments.