Research on coral reef ecosystems has been receiving great attention due to anthropogenic and climate stressors, causing degradation of the ecosystem. While Malaysia is known for its extensive coral reef coverage, the trajectory of its coral reef research trends remained poorly described. Hence, this paper aims to address the state of Malaysian coral reef research using the Web of Science (WoS; 1971–2021, 10,875 publications) database, via hybrid study of meta-analysis with extended review. This will accompany with comparisons against other major coral reef regions globally (sensu Reimer et al., 2019: Red Sea, Great Barrier Reefs, Caribbean, and Ryukyus Islands), and within four areas in the country (East Coast of Peninsular Malaysia, West Coast of Peninsular Malaysia, Sarawak and Sabah). Research papers compiled indicated that Malaysian-based coral reef publication in WoS database is relatively lacking, especially in coral physiology (reproduction) and reef-associated invertebrates (Sponges, bacteria, etc.) whereas its research pool is dominated by Marine Protected Areas studies. East Coast Peninsular Malaysia and Sabah were the dominant study areas for coral reef. Most of the studies were focused on Cnidaria (including reef-building corals), coral reef environments (water quality), and reef-associated fish (Pisces). Additionally, the results showed that research trends are mostly regional-centric within Malaysia, with substantial contrast of interest and limited comparison among distinct marine ecoregions. Hence, comprehensive and collective efforts are needed to establish an ecological research framework. By addressing this, the information from those research data will enable establishment of effective conservation and management strategies.