Protein palmitoylation is a kind of post-translational lipid modification of proteins that widely exists in organisms. Generally, S-palmitoylation occurs mainly through the covalent attachment of palmitic acid to protein-specific cysteine residues via labile thioester linkages. S-palmitoylation is usually reversible because the thioester bond will be hydrolyzed under certain conditions, causing protein depalmitoylation. In addition, S-palmitoylation is closely associated with the occurrence and development of many cardiovascular diseases. This review summarizes the process of protein palmitoylation and depalmitoylation, the relationship between protein palmitoylation and cardiovascular diseases, including arrhythmia, atherosclerosis, pulmonary hypertension, heart failure, and thrombotic diseases, which provide a new direction for cardiovascular disease treatment.