The advancement of heterogeneous catalysts incorporating metal clusters in the nanometric size range has garnered significant attention due to their extraordinary catalytic activity and selectivity. The detailed characterization and understanding of the atomic structure of these metal clusters within catalysts is crucial for elucidating the underlying reaction mechanisms. In the present study, a distinctive three-atom PdNi cluster, characterized by two Pd atoms at terminal positions and a central Ni atom, was synthesized over mordenite zeolite. The presence of atomic PdNi clusters within the eight-membered ring side pocket area was confirmed by multiple advanced analytical techniques, including magic-angle spinning nuclear magnetic resonance spectroscopy, synchrotron X-ray powder diffraction, extended X-ray absorption fine structure spectroscopy, and high-angle annular dark-field scanning transmission electron microscopy. The catalytic activity of the confined active species was examined by the carbene-mediated reactions of ethyl-2-diazoacetate to ethyl-2-methoxyacetate as a model reaction. Compared to the Pd-mordenite and Ni-mordenite, the PdNi-mordenite catalyst incorporates a PdNi cluster, which demonstrates a superior performance, achieving 100% conversion and high selectivity under the same reaction conditions. Our study elucidates the potential of constructing bimetallic clusters in zeolites, providing valuable insights for developing new heterogeneous catalysts applicable to a wide range of catalytic processes.