Gastrointestinal tumors remain the leading causes of cancer-related deaths, and their morbidity and mortality remain high, which imposes a great socio-economic burden globally. Mitochondrial homeostasis depend on proper function and interaction of mitochondrial biogenesis, mitochondrial dynamics (fission and fusion) and mitophagy. Recent studies have demonstrated close implication of mitochondrial homeostasis in gastrointestinal tumorigenesis and development. In this review, we summarized the research progress on gastrointestinal tumors and mitochondrial quality control, as well as the underlying molecular mechanisms. It is anticipated that the comprehensive understanding of mitochondrial homeostasis in gastrointestinal carcinogenesis would benefit the application of mitochondria-targeted therapies for gastrointestinal tumors in future.