In this work, we unravel the beneficial role of the Zn ensemble (in particular, an a single Zn atom) in the sixfold-coordinated kinked (Cu-vacant) site of the stepped Cu(2 1 1) surface for enhancing the reactivity and durability of catalyst in the CH3OH production from CO2 and H2. For such purpose, by using the density functional theory (DFT) and microkinetic modeling methods, we systematically calculate the catalytic properties (activation energy barrier, turn of frequency (TOF), and rate constant), physical properties (cohesive and formation energy) and electronic structures (local density of state, and local charge distribution) of the different defective Cu sites [such as the stepped, kinked, Zn-substituted stepped Cu(2 1 1) surfaces] and the different Zn ensembles [dimer, and linear ensemble].First, our DFT calculations exhibit that the Zn atoms at the sevenfold-coordinated site of the Cu(2 1 1) surface tend to be isolated and acts as the modifier to suppress the loss of Cu atoms from the stepped Cu(2 1 1) surface. Second, we find that the catalysis of CH3OH synthesis strongly depends on the type of defects at the Cu(2 1 1) surface. In particular, the single Zn atom-substituted (sevenfold-coordinated) stepped site in the Cu(2 1 1) surface is found to have the superior catalytic activity (TOF = 3.07 × 10−5 s−1 @ P = 75 bar and T = 523 K) toward the CH3OH formation compared to the traditionally-known active Cu(2 1 1) surface (TOF = 2.73 × 10−7 s−1). In contrast, the sixfold-coordinated kinked site is determined to largely slow down the rate of CH3OH production (TOF = 3.34 × 10−15 s−1). The increased catalysis in the Zn-associated stepped site is related to the significant enhancement of the surface affinity toward the adsorbate having the oxygen moiety (especially, HCOO), which leads to the large reduction of the activation energy barrier in the initial energy-demanding CO2 hydrogenation reaction and in turn the improved catalysis of CH3OH synthesis. Our DFT calculation also elucidates that the stronger covalent-like overlap between O 2p—Zn 3d electrons (which is caused by the electronic charge loss of the Zn atom to the near-neighboring Cu sites) than the O 2p—Cu 3d case is responsible for such enhanced affinity of oxygen-containing adsorbates. In addition, we found that the single Zn atom exhibit the highest activity of CH3OH production (TOFCH3OH = 3.07 × 10−5 s−1) over the dimer (1.62 × 10−7 s−11) and linear ensemble (5.53 × 10−7 s−1), which is related to the weaker affinity of Zn with H than the Cu-H case, which leads to the low coverage of surface H atom and in turn retard the CH3OH production via CH3O hydrogenation.Our study highlights the novel strategy of engineering the activity and stability of the defective undercoordinated kinked site for the enhanced CH3OH synthesis from CO2 and H2 by controlling the arrangement of surface Zn atom at the stepped Cu(2 1 1) surface.