Methamphetamine (MA) can cause brain structural and functional impairment, but there are few studies on whether this difference will sustain on MA abstainers. The purpose of this study is to investigate the correlation of brain networks in MA abstainers. In this study, 47 people detoxified for at least 14 months and 44 normal people took a resting-state functional magnetic resonance imaging (RS-fMRI) scan. A dynamic (i.e., time-varying) functional connectivity (FC) is obtained by applying sliding windows in the time courses on the independent components (ICs). The windowed correlation data for each IC were then clustered by k-means. The number of subjects in each cluster was used as a new feature for individual identification. The results show that the classifier achieved satisfactory performance (82.3% accuracy, 77.7% specificity, and 85.7% sensitivity). We find that there are significant differences in the brain networks of MA abstainers and normal people in the time domain, but the spatial differences are not obvious. Most of the altered functional connections (time-varying) are identified to be located at dorsal default mode network. These results have shown that changes in the correlation of the time domain may play an important role in identifying MA abstainers. Therefore, our findings provide valuable insights in the identification of MA and elucidate the pathological mechanism of MA from a resting-state functional integration point of view.