Coronary artery disease has one of the highest mortality rates in the country, and methods such as thrombolysis and percutaneous coronary intervention (PCI) can effectively improve symptoms and reduce mortality, but most patients still experience symptoms such as chest pain after PCI, which seriously affects their quality of life and increases the incidence of adverse cardiovascular events (myocardial ischaemia-reperfusion injury, MIRI). MIRI has been shown to be closely associated with circadian rhythm disorders and mitochondrial dysfunction. Mitochondria are a key component in the maintenance of normal cardiac function, and new research shows that mitochondria have circadian properties. Traditional Chinese medicine (TCM), as a traditional therapeutic approach characterised by a holistic concept and evidence-based treatment, has significant advantages in the treatment of MIRI, and there is an interaction between the yin-yang theory of TCM and the circadian rhythm of Western medicine at various levels. This paper reviews the clinical evidence for the treatment of MIRI in TCM, basic experimental studies on the alleviation of MIRI by TCM through the regulation of mitochondria, the important role of circadian rhythms in the pathophysiology of MIRI, and the potential mechanisms by which TCM regulates mitochondrial circadian rhythms to alleviate MIRI through the regulation of the biological clock transcription factor. It is hoped that this review will provide new insights into the clinical management, basic research and development of drugs to treat MIRI.