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Coral reefs have high primary productivity and are one of the most important ecosystems in the ocean. However, the health and stability of coral reefs are constantly threatened by climate change and human activities. The coral holobiont is a complex symbiosis between the coral animal, zooxanthellae, and the associated community of microorganisms including bacteria, archaea, viruses, etc. Coral-associated microorganisms are found to be important for the maintenance of coral health, and they are proposed to contribute to the acclimatization and adaptation of reef-building corals under rapid climate change. The coral-microbe interaction mediated by chemical signalling molecules is an important driving force for shaping the microbial communities. Herein, we summarize our current knowledge of the chemical signalling molecules involved in the interaction of the coral holobiont. Specifically, the cooperation and competition among microbes mediated by N-acyl homoserine lactones (AHLs), the interrelationship between microbes and hosts mediated by dimethylsulfoniopropionate (DMSP) and nitric oxide (NO), and the response of corals and microorganisms to reactive oxygen species (ROS) under environmental stresses are highlighted in this review. We further discuss the potential of manipulating the coral microbiome using signalling molecules to restore and protect coral reefs.