Background and objective Stress is an environmental cue, which may lead to increased alcohol craving, and vulnerability to relapse. Heart rate variability (HRV) biofeedback, a supplement standard for inpatient rehabilitation, has been applied for treatment and has been shown to effectively reduce craving and anxiety, increase HRV, and improve vasomotor function, among patients who have alcohol dependence problems. Therefore, the purpose of this study was to investigate the impact of HRV biofeedback and the Phramongkutklao model (PMK model) as an intensive inpatient rehabilitation program concerning stress and craving reduction of inpatients with alcohol use disorder. The findings could benefit treatment design to increase the effectiveness regarding stress and craving reduction among patients with alcohol use disorder and may also reduce rehabilitation costs. Methods We conducted this study as a randomized controlled intervention trial, which was also performed single blinded. In all, 35 patients with alcohol use disorder were recruited and randomly assigned in two groups. Patients in the intervention group (n=17) were treated under the PMK model and underwent 16 sessions of the HRV biofeedback program, which included 30 minute long sessions, 4 days per week, for 4 weeks continuously. Patients in the control group (n=18) received PMK model treatment only. Participants were asked to complete a Stress Test (ST-5) and the Penn Alcohol-Craving Scale at baseline, after completing treatment, and at one month afterward (follow-up). Results The study showed decreased stress and craving in the intervention group immediately after treatment and at one-month follow-up, whereas the control group had reduced stress and craving only immediately after treatment. Furthermore, we found a significant effect concerning stress and craving between baseline and at one-month follow-up that showed the intervention group exhibited higher difference of scores than the control group. Conclusion The study results showed that applying HRV biofeedback may be considered beneficial for standard rehabilitation inpatients to reduce stress and craving for patients with alcohol use disorder.