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Ocean acidification (OA) threatens marine microbial communities that underpin global biogeochemical cycles and marine food webs, however, a systematic synthesis of research progress in this area remains limited. This study presents the first comprehensive bibliometric analysis of ocean acidification impacts on microbial ecology, analyzing 495 Web of Science publications (2005-2025) using CiteSpace to characterize the field’s evolution and identify emerging frontiers. Global collaboration spans 53 countries, led primarily by China, the United States, and Germany, with the GEOMAR Helmholtz Centre for Ocean Research prominent within institutional networks. The research focus has shifted from basic chemical parameters to complex ecosystem processes, with “responses” identified as the most active contemporary research frontier. Overall, the field has matured into a highly internationalized, interdisciplinary domain. We outline four strategic directions for future work: (1) integrating advanceds molecular technologies, including multi-omics and single-cell approaches, to resolve mechanisms; (2) expanding temporal and spatial scales through global observatory networks; (3) quantifying multiple-stressor interactions, particularly with warming and deoxygenation; and (4) connecting molecular processes to biogeochemical cycles at the ecosystem level. These findings provide a data-driven roadmap for next-generation on OA–microbe interactions, essential for predicting marine ecosystem responses to accelerating environmental change and for informing evidence-based ocean conservation policy.