ObjectiveThis study aims to assess the effects of physical training based on the functional near-infrared spectroscopy (fNIRS) and heart rate signals. MethodsThe oxygenated hemoglobin concentration (Delta [HbO2]) signals were recorded from the left prefrontal cortex (LPFC), right prefrontal cortex (RPFC), left motor cortex (LMC) and right motor cortex (RMC) of 23 subjects with methamphetamine (METH) dependencies at resting, spinning training and strength training states. The wavelet phase coherence (WPCO) values were calculated in four frequency intervals: I, 0.6–2; II, 0.145–0.6; III, 0.052–0.145; and IV, 0.021–0.052 Hz. During the spinning training and strength training states, heart rate signals were recorded at 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10 min, respectively. ResultsAfter physical training, the brain regions of LPFC, RPFC and LMC showed different degrees of activation in the subjects with METH dependencies (p < 0.05). The WPCO values between the brain regions significantly altered after spinning training and strength training (p < 0.05) in frequency intervals I, II, III and IV. ConclusionsThe altered WPCO values indicated physical training could affect brain functional connectivity (FC) to a certain extent in the subjects with METH dependencies. These findings provide a method for the assessment of the effects of physical training in FC and will contribute to the development of drug rehabilitation methods in subjects with METH dependencies.