Functional gastrointestinal disorders (FGIDs) encompass a group of disorders characterized by chronic or recurrent gastrointestinal symptoms, while anxiety disorders comprise a class of mental disorders primarily characterized by excessive anxiety and fear. Comorbidity of FGIDs and anxiety disorders has been frequently observed in clinical practice; however, the complex bidirectional relationship between these two disorders remains poorly understood. This review aimed to explore the bidirectional relationship between FGIDs and anxiety disorders, elucidate potential pathophysiological mechanisms, and propose novel diagnostic and therapeutic strategies. Through a review of recent literature, significant reciprocal factors that influence these two disorder categories have been identified. The prevalence of anxiety disorders among FGID patients is substantially higher than that in the general population; additionally, FGID symptoms are more prevalent in individuals with anxiety disorders. The core mechanisms underlying this bidirectional relationship likely involve dysfunction of the brain-gut axis, resulting from nervous, endocrine, and immune system dysfunction. Furthermore, intestinal dysbiosis, genetic factors, and early life stress may play crucial roles in this process. In terms of therapeutic strategies, innovative interventions for the effective management of comorbid FGIDs and anxiety disorders are proposed. Specifically, pharmacological interventions, including the use of selective 5-hydroxytryptamine (5-HT3) receptor antagonists and antidepressants, such as selective serotonin reuptake inhibitors (SSRIs) and serotonin-norepinephrine reuptake inhibitors (SNRIs), can alleviate both gastrointestinal and anxiety symptoms, while psychological interventions, such as cognitive behavioral therapy (CBT) and mindfulness-based stress reduction (MBSR), have also shown efficacy in the reduction of anxiety while significantly improving FGID symptoms. Furthermore, modulation of the gut microbiota through various interventions, such as administration of probiotics and low-Fermentable Oligo-, Di-, Mono-saccharides And Polyols (FODMAP) diets, has also been highlighted as a promising direction for future treatment. Given the collected evidence, the most effective approach would most likely be an integrated therapeutic model, which combines pharmacological, psychological, microbiota modulation, and lifestyle management through a multidisciplinary approach, all of which aim to deliver personalized, comprehensive treatment plans. In summary, the current review elucidates the bidirectional relationship, pathophysiological mechanisms, and novel therapeutic strategies for the treatment of comorbid FGIDs and anxiety disorders, proposing an integrative diagnostic approach that emphasizes screening for anxiety disorders in FGID patients and assessing gastrointestinal symptoms in patients with anxiety disorders. This comprehensive review aimed to provide a theoretical foundation for clinical practice and illuminate directions for future research, ultimately seeking to improve diagnostic and treatment outcomes and quality of life enhancement for this population.