Objective: Methamphetamine use disorder (MUD) is an illness associated with severe health consequences. Virtual reality (VR) is used to induce the drug-cue reactivity and significant EEG and ECG abnormalities were found in MUD patients. However, whether a link exists between EEG and ECG abnormalities in patients with MUD during exposure to drug cues remains unknown. This is important from the therapeutic viewpoint because different treatment strategies may be applied when EEG abnormalities and ECG irregularities are complications of MUD. Methods & Results: We designed a VR system with drug cues and EEG and ECG were recorded during VR exposure. Sixteen patients with MUD and sixteen healthy subjects were recruited. Statistical tests and Pearson correlation were employed to analyze the EEG and ECG. The results showed that, during VR induction, the patients with MUD but not healthy controls showed significant α and β power increases when the stimulus materials were most intense. This finding indicated that the stimuli are indiscriminate to healthy controls but meaningful to patients with MUD. Five heart rate variability (HRV) indexes significantly differed between patients and controls, suggesting abnormalities in the reaction of patient's autonomic nervous system. Importantly, significant relations between EEG and HRV indexes changes were only identified in the controls, but not in MUD patients, signifying a disruption of brain-heart relations in patients. Our findings of stimulus-specific EEG changes and the impaired brain-heart relations in patients with MUD shed light on the understanding of drug-cue reactivity and may be used to design diagnostic and/or therapeutic strategies for MUD.