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Carbocations play crucial roles during catalytic reactions by dictating the reaction pathways and genuine mechanisms, but the instability of carbocations prevents thorough observations. The stabilization of carbocations would greatly help us gain a deep understanding of the reaction mechanisms. By means of ab initio molecular dynamics (AIMD) simulations and an in situ experimental approach, a complete scrambling of 13C-labeled C4 = products was observed during the isomerization reaction in the H-ZSM5 zeolite at room temperature, and the corner-protonated methyl cyclopropanes (as a non-classical carbocation) featuring the three center two-electron (3c–2e) bonds were confirmed to be the highly active metastable intermediates of C4 isomerization. Our results not only uncover the nature of facile C shift in carbocations during zeolite-catalyzed reactions but also bring some fundamental understandings to carbocation chemistry in a zeolite confined environment