Metal clusters represent a promising class of catalysts for various reactions, but the simultaneous improvement of their stability and catalytic activity is a longstanding challenge. Herein, we created a stable dual-cluster metal-organic framework (MOF) that featured atomically synergistic bimetallic pair sites colocalized within sub-nanometer pockets. The pair sites, consisting of Ni and Mo sites respectively originating from defective MOF and Polyoxometalate (POM) clusters, were rationally constructed by size-matched ligand exchange. The as-obtained dual-cluster MOF (MnMo₆-lg-PCN-601) exhibited superior catalytic activity, rate performance (t_1/2 < 1 min, TOF = 140 min⁻¹), and stability toward the degradation of the chemical warfare agent simulant 2-chloroethyl ethyl sulfide (CEES). In-situ Fourier transform infrared (FTIR) studies and density functional theory (DFT) calculations demonstrated that the atomic synergy between colocalized pair sites favored the adsorption and activation of the CEES substrate, moreover, it also promoted H₂O₂ decomposition for the selective oxidation of CEES. Our work opens a new avenue for the construction of stable metal clusters with high catalytic activity for application in various multi-substrate reactions.