Highly active subnano Pd clusters were synthesized using i-motif DNA as the template through characterization via ESI MS, DLS, XPS, UV-vis, and FTIR. It is indicated that Pd1-Pd5 clusters are generated at a [Pd]/[base] ratio of 0.2, Pd8 to Pd9 clusters are generated at a [Pd]/[base] ratio of 0.5, and large nanoparticles with the size about 2.6 nm are formed at a [Pd]/[base] ratio of 2.0. The i-motif-stabilized Pd8-Pd9 clusters show high catalytic activity toward the reduction of 4-nitrophenol with a relative rate constant value of 2034 min(-1) (mM Pd)(-1). DFT calculations disclose that the unique structure of the i-motif with consecutive hemiprotonated CH(+)·C pairs can efficiently ligate Pd ions at the N3 sites of cytosines and that the synthesized Pd clusters consist of metallic Pd atoms as well as positively charged Pd that is ligated by nucleobases, which is capable of facilitating the activation of the nitryl group of 4-nitrophenol. This work suggests a promising pathway to preparing subnano metal catalysts with enhanced catalytic activity using programmable DNA scaffolds.