Previous studies have shown that perennial Chan training leads to improvements in brain functioning. However, few studies have investigated the effects of short-term Huatou Chan training. The current study explored the effects of a three-day Huatou Chan training on physical and emotional health, as well as brain state. Seventy healthy subjects were recruited and divided into two groups: the Huatou Chan group and the Control group. The Huatou Chan group received a 3-day Huatou Chan training, while the Control group waited for three days. Both groups completed a 6-min Brain State Index recording, the SCL-90, the Brief Profile of Mood State, the Meaning in Life Questionnaire, and the Index of Well-being, prior to and after the training or waiting period. Results showed that short-term Huatou Chan training had significant benefits on physical and emotional health (somatization, obsessive-compulsive, depression, hostility, and psychoticism), negative emotions (tension-anxiety, depression-dejection, anger-hostility, fatigue-inertia, and confusion-bewilderment), well-being, and attitude towards life. In addition, short-term Chan training can significantly improve brain state, as shown by the index of depression, anxiety, alerting, intelligence, and sleep disorder. To our knowledge, this is the first study to provide direct evidence for the benefits of short-term intensive Huatou Chan training on physical and mental health.