Copper nanoparticles (Cu NPs) are commonly used as catalyst active components in CO2 hydrogenation reactions. However, they often lose their catalytic activity due to sintering in most reaction environments. This study explores a solution for Cu-supported catalysts used for methanol production from CO2 hydrogenation by fixing Cu NPs in the mesopores generated in zeolite. Mesopores were generated in NaY zeolite by partially dealuminating its framework. High-resolution (scanning) transmission electron microscopy (HR(S)TEM) and CO adsorption measurements confirm that the synthesized mesoporous zeolite-supported Cu NPs are highly dispersed and fixed within the mesopores. In comparison with conventional microporous zeolite-supported Cu NPs (2 wt%), Cu NPs (2 wt%, average size of 2.2 nm) in mesoporous zeolite increased methanol production from ∼26 mmolgCu−1h−1 to approximately 56 mmolgCu−1h−1 at 250 °C. By further modifying the mesoporous zeolite with Zr (2 wt%), Cu NPs increased in size, and the methanol production rate increased approximately 2.2 folds to 125 mmolgCu−1h−1 under similar conditions due to zeolite electronic modification and the newly formed Zr-zeolite/Cu interface. However, the addition of Zr significantly increased the Cu NP size and moved part of them out of the mesopores, lowering their stability. In situ DRIFTS experiments reveal CO2 hydrogenation proceeds through the formate route via a direct formation of dominantly carbonate (*CO3), which hydrogenates to formate (*HCOO) and traces of methoxy (*H3CO), and subsequently methanol (CH3OH). This study reports the design of active and stable catalysts for CO2 hydrogenation to methanol by engineering Cu NPs in zeolite pores