OBJECTIVE: To observe the improvement of acupuncture and moxibustion on symptoms of qi-deficiency syndrome as well as their differences on the parameters of heart rate variability (HRV). METHODS: Thirty patients with qi-deficiency syndrome and 15 healthy volunteers were recruited. Thirty patients with qi-deficiency syndrome were randomly assigned into an acupuncture group and a moxibustion group, 15 cases in each one. Fifteen healthy volunteers were allocated as a healthy control group. Patients in the acupuncture group and healthy control group were treated with acupuncture while patients in the moxibustion group were treated with moxibustion. Guanyuan (CV 4) and Zusanli (ST 36) were chosen for treatment, once every other day, for totally 10 times. All the patients were evaluated with qi-deficiency assessment scale (QDAS) and HRV parameters before treatment, after 4th treatment and after all treatment. The correlation was analyzed between QDAS and HRV parameters, and HRV parameters were compared among the three groups before treatment, after 4th treatment and after all treatment. RESULTS: Compared before treatment, the scores of QDAS were decreased in the acupuncture group and the moxibustion group after 4th treatment and after all treatment (all P<0.05); after all treatment the score of QDAS in the moxibustion group was lower than that in the acupuncture group (P<0.05). The HRV parameters of qi-deficiency syndrome were significantly lower than those of healthy volunteers with higher correlation with QDAS. Compared before treatment, the mean heart rate was decreased after treatment (P<0.05), while total HRV and low frequency were increased in the moxibustion group (both P<0.05). The mean heart rate in the healthy control group was increased after treatment (P<0.05). The differences of HRV parameters before and after treatment were not significant in the acupuncture group (all P>0.05). CONCLUSIONS: Total HRV can reflect the severity of qi-deficiency syndrome. Both acupuncture and moxibustion can improve symptoms of qi-deficiency patients, which is superior in moxibustion. The possible mechanism is likely to be related with improved sustainable activation of autonomic nervous system.