Enzyme mimics are of significant importance due to their facile preparation, low cost and stability to rigorous environments. Molecularly imprinted polymers (MIPs) have been important synthetic mimics of enzymes. However, effective strategies for the rational design of enzyme-mimicking MIPs have still remained limited. Herein, we report a new strategy, termed affinity gathering-enhanced coupling and thermal cycling amplification (AGEC-TCA), for the rational design and engineering of molecularly imprinted mesoporous silica nanoparticles (MSNs) that are capable of ligating short ssDNA fragments. This strategy relied on enhancing the effective collision probability via binding substrates into highly favorable orientation by product-imprinted MSNs as well as product release via thermal cycling which enabled successive product amplification. Using modified and natural hexadeoxyribonucleotide as templates, the prepared product-imprinted MSNs exhibited a remarkably enhanced reaction speed (by up to 63-fold) as well as excellent sequence specificity towards substrate trideoxyribonucleotides. Thus, this strategy opened up a new avenue to access enzyme mimics via molecular imprinting.