Understanding efficiency–durability relationships and related mitigation strategies is an important step toward the commercialization of organic photovoltaics (OPVs). Here, we report that a photoactivated 6-bridged azide cross-linker (6Bx) improves the morphological stability by suppressing the thermally activated diffusion of (Y6) acceptor molecules in PM6:Y6 bulk-heterojunction (BHJ)-based OPVs. Cross-linked PM6:Y6 (0.05 wt % 6Bx) BHJ OPVs retain 93.4% of the initial power conversion efficiency upon thermal aging at 85 °C for 1680 h (T80 = 3290 h). Molecular origins of enhanced thermal stability are corroborated by optical spectroscopy, surface imaging, 2D solid-state nuclear magnetic resonance (ssNMR), Raman spectroscopy, scanning electron diffraction (SED) measurements, and analysis of the BHJ thin films. The facile single-step cross-linking strategy in conjugation with advanced characterization methods presented in the study paves the way toward developing durable OPVs based on non-fullerene acceptors (NFAs).