Ocean alkalinity enhancement (OAE) is a leading climate mitigation strategy for atmospheric carbon dioxide removal, with theoretical potential to sequester gigatons of CO₂ annually while counteracting ocean acidification. Yet, as a deliberate anthropogenic perturbation to the marine carbonate system, the ecological consequences for the microbial communities that underpin marine biogeochemical cycles remain incompletely understood. Alterations in seawater pH and carbonate saturation states could influence microbial assemblages, with implications for ecosystem functioning and stability under global climate change. In this study, we experimentally assessed the responses of marine prokaryotic communities to unequilibrated alkalinity additions (85–495 µmol kg^-1) using Mg(OH)₂ in the subtropical South China Sea. Across both microcosm (55 L) and mesocosm (50,000 L) scales during the wet and dry seasons, a total alkalinity increase of 80–427 µmol kg^-1 substantially elevated pH (8.57–8.77) and carbonate saturation states. Despite these pronounced chemical perturbations, the prokaryotic diversity, community structure, and predicted metabolic functions remained remarkably stable. This stability persisted across different experimental scales and contrasting seasonal conditions. Instead, seasonal variability and nutrient availability were the dominant drivers of microbial community shifts, overwhelming the minor effects of alkalinity addition. Our findings align with recent studies from the North Atlantic and the Equatorial Pacific, suggesting that the resilience of prokaryotic communities to moderate, unequilibrated OAE is a robust, globally relevant phenomenon. This study emphasizes that even under relatively intense OAE scenarios, microbial community stability may help sustain ecosystem functioning amid emerging ocean-based carbon dioxide removal interventions, a key finding for developing effective Monitoring, Reporting, and Verification (MRV) frameworks.