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Converting CO2 into methanol on a large scale is of great significance in the sustainable methanol economy. Zirconia species are considered to be an essential support in Cu‐based catalysts due to their excellent properties for CO2 adsorption and activation. However, the evolution of Zr species during the reaction and the effect of their structure on the reaction pathways remain unclear. Herein, single‐site Zr species in an amorphous SiO2 matrix are created by enhancing the Zr−Si interaction in Cu/ZrO2‐SiO2 catalysts. In situ X‐ray absorption spectroscopy (XAS) reveals that the coordination environment of single‐site Zr is sensitive to the atmosphere and reaction conditions. We demonstrate that the CO2 adsorption occurs preferably on the interface of Cu and single‐site Zr rather than on ZrO2 nanoparticles. Methanol synthesis in reverse water‐gas‐shift (RWGS)+CO‐hydro pathway is verified only over single‐dispersed Zr sites, whereas the ordinary formate pathway occurs on ZrO2 nanoparticles. Thus, it expands a non‐competitive parallel pathway as a supplement to the dominant formate pathway, resulting in the enhancement of Cu activity sixfold and twofold based on Cu/SiO2 and Cu/ZrO2 catalysts, respectively. The establishment of this dual‐channel pathway by single‐site Zr species in this work opens new horizons for understanding the role of atomically dispersed oxides in catalysis science. [ABSTRACT FROM AUTHOR]