Inflammatory Bowel Disease (IBD) is a chronic relapsing inflammatory condition of the intestine, characterized by symptoms such as chronic diarrhea, abdominal pain, and weight loss. The pathogenesis of IBD is complex, with mitochondrial dysfunction being considered a key factor in its onset, progression, and persistence. Mitochondria, as the primary energy suppliers within cells, not only produce adenosine triphosphate (ATP) but also play crucial roles in regulating cellular metabolism, maintaining redox balance, and controlling cell death processes. Targeting mitochondria to regulate mitochondrial functions, including energy metabolism, oxidative stress, mitophagy, dynamics, and biogenesis, as well as maintaining the dynamic balance of the “gut microbiota-mitochondria axis,” has emerged as a promising strategy for the prevention and treatment of IBD. Traditional Chinese Medicine (TCM) has shown potential multi-target regulatory properties in preclinical studies; however, robust clinical validation and target-specific pharmacological evidence remain limited. This review explores the mechanisms and underlying connections between mitochondrial dysfunction and IBD, summarizing the current research on how active metabolites of TCM modulate mitochondrial dysfunction in the prevention and treatment of IBD. It provides new insights into the pathogenesis of the disease and opens up new avenues and strategies for the prevention, treatment, and research on IBD treatment with TCM.