Background: Warm acupuncture therapy in Mongolian medicine is an important component of traditional Mongolian medicine, characterized by acupuncture and warm stimulation. Based on the three theories (Heyi, Xila, Badagan) and the principle of cold heat balance, it regulates the circulation of qi and blood and immune function in the human body, and is widely used to treat cold diseases, joint diseases, and neurological diseases. Its history can be traced back to the “moxibustion technique” recorded in the “Huang Di Nei Jing” during the Qin and Han dynasties, and through long-term practice, it has integrated traditional Chinese medicine meridian theory with nomadic medical experience to form a unique diagnosis and treatment system. Modern research has shown that warm acupunctures exhibit significant analgesic, anti-inflammatory, and neuroprotective effects through their thermal effects and multi-target regulation of the neuroendocrine immune network. However, their molecular mechanisms and clinical translation still need to be systematically investigated. Aim: This study aims to synthesize recent research results, clarify the mechanism of action of Mongolian medicine warm acupuncture (such as neurotransmitter regulation, gene expression regulation, gut microbiota intervention, etc.), summarize its clinical application progress in painful diseases, mental disorders, and osteoarthritis, and explore the optimization path of modern technology for traditional therapies, providing theoretical basis for improving the standard of efficacy and promoting internationalization. Materials and Methods: Combining literature analysis with experimental research, integrating multidisciplinary evidence. Results: Mechanism of action: Neuroregulation: Warm acupuncture inhibits PAX8 (Paired Box Gene 8) protein expression by upregulating miR-101a, improves hippocampal neuron activity, and regulates the sleep wake cycle; Activate the brain gut axis, promote the production of short chain fatty acids, increase serum 5-HT (5-Hydroxytryptamine) levels, and alleviate depressive symptoms. Anti-inflammatory and analgesic: reduce pro-inflammatory factors such as IL-6 (Interleukin-6) and TNF – α (Tumor Necrosis Factor-alpha, inhibit COX-2 (Cyclooxygenase-2) activity, and block pain signal transduction. Immune regulation: Enhance macrophage phagocytic function, balance TH1/TH2 cell (T helper cell type 1/ T helper cell type 2) ratio, and improve immune disorders induced by chronic stress. Clinical application: Pain related diseases: The total effective rate of treating knee osteoarthritis is 94.7%, significantly relieving morning stiffness and limited mobility; Reduce VAS scores for lower back and leg pain in patients with lumbar disc herniation by more than 40%. Neurological disorders: Improve the sleep quality of elderly insomnia patients and regulate serum NPY (Neuropeptide Y) and 5-HT1A levels; Relieving tinnitus symptoms may be related to improving ear microcirculation. Mental disorders: improve behavioral abnormalities in depressed rats by regulating gut microbiota (such as increasing the abundance of SCFAs producing bacteria) and brain gut peptide secretion. Conclusion Mongolian medicine warm acupuncture exerts therapeutic effects through multiple targets and pathways, combining traditional medical characteristics with modern scientific verification. It has significant advantages in pain management and intervention for mental illnesses. In the future, it is necessary to further deepen its molecular mechanism research, promote device standardization, and expand its application in chronic disease rehabilitation and preventive medicine, providing scientific support for the modernization of ethnic medicine.