Inflammatory bowel disease (IBD) is a chronic and relapsing inflammatory disorder of the gastrointestinal tract that poses a significant threat to human health. The pathogenesis of IBD remains unclear and is believed to involve various factors, including genetics, immune dysregulation, and environmental triggers. Recent evidence has highlighted the role of mitochondrial damage and dysfunction in the development of IBD. This article provides a comprehensive review and overview of studies related to the role of mitochondrial damage in IBD, focusing on the effects of mitochondrial oxidative stress damage, autophagy dysfunction, kinetic disturbances, and respiratory defects. The aim is to identify potential therapeutic targets and provide new insights for the scientific prevention and treatment of IBD.