To investigate the relieving effects of hot spring balneotherapy on mental stress, sleep disorder, general health problems, and women's health problems in sub-healthy people, we recruited 500 volunteers in sub-health in Chongqing, and 362 volunteers completed the project, including 223 in the intervention group and 139 in the control group. The intervention group underwent hot spring balneotherapy for 5 months, while the control group did not. The two groups took questionnaire investigation (general data, mental stress, emotional status, sleep quality, general health problems, as well as some women's health problems) and physical examination (height, weight, waist circumference, blood pressure, blood lipid, blood sugar) 5 months before and after the intervention, respectively. After intervention, sleep disorder (difficulty in falling asleep (P = 0.017); dreaminess, nightmare suffering, and restless sleep (P = 0.013); easy awakening (P = 0.003) and difficulty in falling into sleep again after awakening(P = 0.016); and mental stress (P = 0.031) and problems of general health (head pain (P = 0.026), joint pain(P = 0.009), leg or foot cramps (P = 0.001), blurred vision (P = 0.009)) were relieved significantly in the intervention group, as compared with the control group. While other indicators (fatigue, eye tiredness, limb numbness, constipation, skin allergy) and women's health problems (breast distending pain; dysmenorrhea, irregular menstruation) were relieved significantly in the self-comparison of the intervention group before and after intervention (P < 0.05), but showed no statistically significant difference between two groups (P > 0.05). All indications (except bad mood, low mood, and worry or irritability) in the intervention group significantly improved, with effect size from 0.096 to 1.302. Multiple logistic regression analysis showed that the frequency, length, and location of balneotherapy in the intervention group were the factors influencing emotion, sleep, and health condition (P < 0.05). Relief of insomnia, fatigue, and leg or foot cramps was greater in old-age group than in young-aged group (P < 0.05). Physical examination found that waist circumferences in women of various ages under 55 years were significantly reduced in the intervention group (P < 0.05), while that in men did not significantly change (P > 0.05). Spa therapy (balneotherapy) relieves mental stress, sleep disorder, general health, and reduces women's waist circumferences in sub-healthy people.