We investigate the atmospheric production and subsequent detection of sub-GeV dark mesons within the framework of a confining dark sector coupled to the Standard Model (SM) via a vector portal. High-energy cosmic ray interactions in the atmosphere produce dark quarks through proton bremsstrahlung, rare decay of Standard Model mesons, and Drell-Yan processes, which subsequently hadronize into dark mesons. We adopt a modified Quark Combination Model to describe the non-perturbative dark hadronization process, allowing for a detailed event-level characterization of the dark meson flux. We simulate the flux and the interaction of these relativistic dark mesons in the Jiangmen Underground Neutrino Observatory (JUNO) using the GENIE generator, considering both elastic scattering off nuclei and deep inelastic scattering channels. Based on the projected 20 ktonyear exposure, we derive sensitivity limits on the coupling strength between the dark gauge boson and the SM sector. Our results demonstrate that JUNO can probe substantial unexplored parameter space, particularly for light mediators ( MeV), where it achieves sensitivities to the portal interaction as low as .

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