AbstractZeolites are three-dimensional aluminosilicates having unique properties from the size and connectivity of their sub-nanometer pores, the Si/Al ratio of the anionic framework, and the charge-balancing cations. The inhomogeneous distribution of the cations affects their catalytic performances because it influences the intra-crystalline diffusion rates of the reactants and products. However, the structural deformation regarding inhomogeneous active regions during the catalysis is not yet observed by conventional analytical tools. Here we employ in situ X-ray free electron laser-based time-resolved coherent X-ray diffraction imaging to investigate the internal deformations originating from the inhomogeneous Cu ion distributions in Cu-exchanged ZSM-5 zeolite crystals during the deoxygenation of nitrogen oxides with propene. We show that the interactions between the reactants and the active sites lead to an unusual strain distribution, confirmed by density functional theory simulations. These observations provide insights into the role of structural inhomogeneity in zeolites during catalysis and will assist the future design of zeolites for their applications.