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High dispersion of active metal is always approved for better catalytic performance in CO2hydrogenation to methanol. Herein, a strategy was proposed to encapsulate copper nanoparticles in supercages of zeolite 13X, and hence the growth of copper nanoparticles can be controlled. In the present work, catalysts were prepared using ion-exchange and hydrogen reduction at a tiny positive pressure. The results show that as-synthesized catalyst consists of metallic copper and FAU-type zeolite. Excessive amount of copper will destroy zeolite frameworks, and the amount of 5.9 at% is appropriate for considerable BET surface area and ideal copper dispersion. Meanwhile, copper nanoparticles may grow outside from zeolite at high reduction temperatures (≥220 °C), resulting in serious surface area decline and metallic copper agglomeration. Afterwards catalytic tests reveal good stability of the optimal CX-220 catalyst in continuous reactions. The CX-220 achieves remarkably high methanol selectivity of ≥ 95% within wide ranges of reaction temperatures and reaction pressures. Further analyses reveal that the encapsulation of copper nanoparticles reduces micropores and enriches mesopores in zeolite. The apparent activation energy for methanol synthesis over CX-220 catalyst has been lowered to a very low level because of the unique microstructure, and thus the methanol synthesis reaction is dominant in CO2hydrogenation for dramatic methanol selectivity. Therefore, this work gives important insights and applicable routes for catalysts analyses of CO2hydrogenation to methanol.