Coronary heart disease (CHD) is a leading cause of death worldwide. It is a multifactorial disorder resulting from harmful interactions between genetic and environmental factors. Due to the central role of mitochondria in cellular energy homeostasis, there is growing evidence supporting the role of damage to mitochondrial components such as mitochondrial DNA (mtDNA) in the pathogenesis and progression of CHD. However, the molecular mechanisms linking mtDNA and CHD remains unknown. In terms of mutations, we found that mitochondrial transfer RNA (mt-tRNA) genes are hot spots for pathogenic mutations associated with CHD. These mutations cause structural and functional changes in tRNA; specifically, failure of tRNA metabolism may impair mitochondrial protein synthesis and lead to mitochondrial dysfunction responsible for CHD. This review provides a detailed summary of the mtDNA mutations that have been reported to be associated with CHD and further discusses the possible molecular mechanisms behind the involvement of these mtDNA mutations in CHD.