Difficulties in identifying and regulating emotion are recognized as major factors of relapse in alcohol use disorders (AUD). This study aimed to evaluate the differences of emotion regulation processes in AUD patients with short-term (STA, less than one month) and long-term abstinence (LTA, at least six months) by recording the high frequency of Heart Rate Variability (HF-HRV) in response to emotional and neutral stimuli. Emotional induction constituted the presentation of highly emotional and neutral pictures (IAPS data base) presenting human interactions. HF-HRV was recorded before (at rest), during (pictures) and after emotional induction (recovery). The results showed higher phasic HF-HRV in the STA group in comparison to the LTA and C groups for negative, positive and neutral stimuli. In the LTA group, we observed a normalization of HRV, in response to emotional stimuli. However, for negative valence stimuli in the recovery period, LTA participants are no more different from STA group. A main positive correlation was observed for both patient groups between craving scores and increased HF-HRV during and after the emotion induction. The data support the hypothesis of emotion regulation impairment after STA but also show a partial improvement with prolonged abstinence. This impairment in patients may correspond to the maintenance of negative feedback that accentuates the difficulties in the emotional physiological process and limits the ability to engage in or maintain other processes. HF-HRV is a good indicator of emotion regulation processes related to the intensity of the craving even after long-term abstinence.