Methamphetamine (MA) addiction is a chronic neurotoxic brain disorder that places a significant burden on public health, with a high relapse risk. Long-term abstinence can significantly reduce craving, yet the potential alterations caused by long-term abstinence still remain unclear. In this study, a total of 62 MA users who underwent longitudinal follow-up during their period of long-term abstinence (duration of long-term abstinence: 347.52 ± 99.25 days) were enrolled. For the first time, we employed a promising framework known as network control theory to explore the impact of long-term abstinence on MA addicts. Our observations indicated that long-term abstinence led to a decline in the control energy required for transitions from the visual network, and somatomotor network to the frontoparietal network, suggesting a reduced barrier for triggering executive control response to the drug cues. Furthermore, we identified the orbitofrontal cortex and the dorsolateral prefrontal cortex as crucial regions involved in facilitating these transitions. Notably, we discovered significant associations between the influence of long-term abstinence on brain regions and the spatial distribution of key biological factors, such as DAT, 5HTT, D2, MOR, VAChT, and NET. Overall, our findings not only provide a novel perspective on understanding the impact of long-term abstinence in MA addicts but also link this process to biological factors.