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 such as genetics, immune dysregulation, and environmental triggers. In recent years, increasing evidence has highlighted the role of mitochondrial damage and dysfunction in the development of IBD. This review provides a comprehensive review and overview of studies related to mitochondrial damage in inflammatory bowel disease, focusing on the effects of mitochondrial oxidative stress damage, autophagy dysfunction, kinetic disturbances, and respiratory defects on IBD. The aim is to identify potential therapeutic targets and provide new insights for the scientific prevention and treatment of IBD.