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CO2 reduction has been pursued for decades as an effective way to produce useful fuels and to mitigate global warming at the same time. Methanol synthesis from CO2 hydrogenation over Cu-based catalysts plays an important role in the chemical and energy industries. However, fundamental questions regarding the reaction mechanism and key reaction intermediates of this process are still unclear. To address these issues, we studied the CO2 hydrogenation process using density functional theory (DFT) combined with van der Waals (vdW) force corrections, finding that the most effective pathway proceeds along the reaction series CO* → CHO* → CH2O* → CH2OH* → CH3OH* with the reactive intermediate CH2O*, which is consistent with experimental findings. Additionally, we find that water molecules play an inhibiting role in the reaction, while H bonds and vdW forces have an essential effect on the reaction mechanisms. These findings shed light on the reaction mechanism of CH3OH formation from CO2 hydrogenation and reveal the essence of H2O in this reaction, providing a useful basis for preceding studies.