Climate change related coral reef research has been receiving great interest globally as the world continues to experience worsening catastrophic climate change events, which causes the degradation of the ecosystem. While Malaysia is known for its extensive coral reef coverage, little is known about its coral reef research trajectory, especially related to climate change. Hence, this study aims to address the state of Malaysian coral reef research trend using the Web of Science (WoS; 1987–2022) database with comparison made within four areas in the country (East Coast of Peninsular Malaysia, West Coast of Peninsular Malaysia, Sarawak and Sabah), and explicitly looking into the aspect of climate change using three search strings respectively; (1) Bleach*, (2) Acid*, (3) Climate Change*. The results found the number of such publications in the WoS database is low (total of 31 publications in 36 years), with substantial research location bias dominated at the East Coast of Peninsular Malaysia. Generally, the study subjects of the publications focus on mixed organisms (Coral Reef) and Cnidaria as well as non-biological category ‘Environment’. Overall, the ecological assessment of the study trend shows notable climate change research gap in Malaysian coral reef research (lack of important organism studies; Pisces, Echinodermata, Mollusca). Thus, there is a need for climate change inclusive research direction in Malaysian coral reef research for the understanding, adaptation, prediction, and management of our coral reef ecosystem in an era of accelerated climate change circumstances.