<p>Proton transport is a multiscale phenomenon critical to chemistry, physics, biology and materials science, yet development of a high-fidelity multiscale model bridging quantum to mesoscale dynamics remains a major challenge owing to reactive bonding rearrangements in the Grotthuss proton shuttling. Here we present the Hydronium Ultra-coarse-grained Model with Improved Dynamics (HUMID), which enables the investigation of hydrated protons across much larger spatiotemporal scales via bottom-up coarse-graining (CG) that recapitulates structure and dynamics at a reduced resolution. The unique structural correlations and dynamics arising from the hydronium cation are captured by introducing internal states to the CG sites, as derived from quantum mechanics, with a systematic design principle for determining these internal states. HUMID accurately reproduces diffusion and hydronium time correlation functions with a three-order-of-magnitude computational speedup. This model enables the study of mesoscale phenomena governed by proton transport and establishes design principles for reactive CG models.</p>