Abstract: Objective: Exercise was considered to be able to regulate the brain, heart and drug craving of methamphetamine(MA)addicts, but the internal relationship and influencing mechanism of the variables needed to be further explored. Methods: Fifty-five male MA addicts in a drug rehabilitation education and correction center in Chongqing were selected. They were randomly divided into the aerobic + resistance training group, compound aerobic training group, and control group. The EEG and HRV instruments were used to collect the alpha wave energy value and HRV activity of the prefrontal brain area in different cue exposure tasks, and an analog rating scale(VAS) was used to assess cravings. Results: 1) After 12 weeks of intervention, the drug cravings in the aerobic + resistance training group and the compound aerobic training group were significantly lower than those in the control group. 2)Compared with the neutral task, the Fz-alpha wave energy value, RMSSD and HFn of the three groups of dependents were significantly lower in the drug task, but the LFn was significantly higher at baseline; after intervention, the Fz-alpha, F3-alpha, and F4-alpha wave of the two exercise groups in the drug task were significantly higher than that of the control group, and the SDNN,RMSSD, and HFn in drug and neutral tasks were significantly higher than that of the control group, and Fz-alpha wave, RMSSD,LFn and HFn had no significant difference in cue task; there was no significant difference in prefrontal alpha wave energy and HRV between the two exercise groups in drug and neutral tasks; the F3-alpha wave of the compound aerobic training group in the neutral task and the F4-alpha wave of the aerobic + resistance training group were significantly higher than the baseline level; there were no significant changes in the prefrontal alpha wave energy and HRV of the control group in the drug and neutral tasks after the intervention.3) In the drug and neutral tasks, the alpha wave energy value of the prefrontal brain area in the two exercise groups was positively correlated with SDNN, RMSSD, and HFn, and negatively correlated with LFn after intervention, but the correlation in the control group was weak; the drug craving of the three groups was negatively correlated with the alpha wave, SDNN, RMSSD, and HFn in the prefrontal brain area, and positively correlated with LFn. Conclusions: Acute drug exposure could induce abnormal activation of frontal midline and autonomic nerves in MA addicts, while moderate-intensity aerobic combined with resistance training and compound aerobic training could improve the abnormal activation of prefrontal brain regions in addicts when facing stimulation,which can help to maintain the coordinated activation of the brain-heart system in a specific situation, thereby effectively reducing the drug craving in MA addicts, but there was no significant difference in the effectiveness of the two exercise prescriptions.