Mitochondria are heterogeneous and essentially contribute to cellular functions and tissue homeostasis. Mitochondrial dysfunction compromises overall cell functioning, tissue damage, and diseases. The advances in mitochondrion biology increase our understanding of mitochondrial dynamics, bioenergetics, and redox homeostasis, and subsequently, their functions in tissue homeostasis and diseases, including cardiometabolic diseases (CMDs). The functions of mitochondria mainly rely on the enzymes in their matrix. Sirtuins are a family of NAD+-dependent deacylases and ADP-ribosyltransferases. Three members of the Sirtuin family (SIRT3, SIRT4, and SIRT5) are located in the mitochondrion. These mitochondrial Sirtuins regulate energy and redox metabolism as well as mitochondrial dynamics in the mitochondrial matrix and are involved in cardiovascular homeostasis and CMDs. In this review, we discuss the advances in our understanding of mitochondrial Sirtuins in mitochondrion biology and CMDs, including cardiac remodeling, pulmonary artery hypertension, and vascular dysfunction. The potential therapeutic strategies by targetting mitochondrial Sirtuins to improve mitochondrial function in CMDs are also addressed.