Synthesizing atomically dispersed synergistic active pairs is crucial yet challenging in developing highly active heterogeneous catalysts for various industrially important reactions. Here, a single molecular Re species is immobilized on the inner surface of a Y zeolite with Brønsted acid sites (BASs) within atomic proximity to form Re OMS–BAS active pairs for the efficient catalysis of olefin metathesis reactions (OMS: olefin metathesis site). The synergy within the active pairs is revealed by studying the coadsorption geometry of the olefin substrates over the active pairs by synchrotron X-ray and neutron powder diffraction. It is shown that the BAS not only facilitates olefin adsorption but also aligns the olefin molecule to the Re OMS for efficient intermediate formation. Consequently, for the cross-metathesis of ethene and trans-2-butene to propene, this catalyst shows high activity under mild reaction conditions without observable deactivation. The catalyst outperforms not only traditional ReOx-based catalysts but also the best industrially applicable WOx-based catalyst thus far that we discovered previously. The concept of using two isolated active sites of different functionalities within atomic proximity in a confined cavity can provide opportunities for designing synergistically catalytic materials.