To observe the clinical effect and safety of the warm acupuncture of Mongolian medicine in treatment of insomnia in the elderly, and to explore its underlying brain-gut peptide mechanism. Sixty elderly patients with insomnia were randomly divided into a warm acupuncture group and a western medication group, 30 cases in each group. In the warm acupuncture group, the warm acupuncture of Mongolian medicine was operated at Dinghuixue (at the center of the vertex, the crossing site of the anterior midline and the line connected the upper edges of two ear apexes), Heyixue (at the depression of the spinous process of the 7th cervical vertebra) or Xinxue (at the depression of the spinous process of the 6th thoracic vertebra) in each treatment. Only one of the above points was selected and stimulated for 20 min one treatment and the three points were used alternatively. The treatment was given once every day or every other day, 3 times a week, and for a total of 3 weeks. In the western medication group, estazolam tablets were administered orally, once a day, 1 mg before bedtime, consecutively for 3 weeks. Before and after treatment, as well as in 1-month follow-up visit after the treatment completion, the scores of the Pittsburgh sleep quality index (PSQI) and the insomnia severity index (ISI) were observed in the two groups. The serum brain-related peptide markers (substance P [SP], neuropeptide Y [NPY], 5-hydroxytryptamine 1A [5-HT1A] and 5-hydroxytryptamine 2A [5-HT2A]) were measured before and after treatment, and the clinical efficacy and safety was evaluated in the two groups. After treatment and in follow-up, the scores of sleep quality, sleep latency, sleep duration, sleep efficiency, sleep disturbance and daytime dysfunction, as well as the total scores of PSQI, and ISI scores were all reduced in the two groups (P<0.05, P<0.01); and the scores in the warm acupuncture group were lower than those of the western medication group (P<0.05, P<0.01). After treatment, the levels of serum SP and 5-HT2A were decreased (P<0.01) and the levels of serum NPY and 5-HT1A were increased (P<0.01) when compared with those before treatment in the two groups. The levels of serum SP and 5-HT2A in the warm acupuncture group were lower than those of the western medication group (P<0.05), and the levels of serum NPY and 5-HT1A were higher than those of the western medication group (P<0.05). After treatment, the total effective rate was 93.3% (28/30) in the warm acupuncture group, which was higher than 83.3% (25/30) of the western medication group (P<0.05). No serious adverse reactions were found in the two groups. Warm acupuncture of Mongolian medicine can effectively improve the sleep quality of the elderly patients with insomnia, and its mechanism may be related to the regulation of the levels of serum SP, NPY, 5-HT1A and 5-HT2A.