Methamphetamine use disorder (MUD) is a chronic brain disorder that involves frequent failures of inhibitory control and relapses into methamphetamine intake. However, it remains unclear whether the impairment of inhibitory control in MUD is proactive, reactive or both. To address this issue, the current study used the conditional stop-signal task to assess proactive and reactive inhibitory control in 35 MUD patients with long-term abstinence and 35 matched healthy controls. The results showed that MUD patients with long-term abstinence had greater preparation costs than healthy controls, but did not differ in performance, implying a less efficient utilization of proactive inhibitory control. In contrast, MUD patients exhibited intact reactive inhibitory control; reactive but not proactive inhibitory control was associated with high sensation seeking in MUD patients with long-term abstinence. These findings suggest that proactive and reactive inhibitory control may be two different important endophenotypes of addiction in MUD patients with long-term abstinence. The current study provides new insight into the uses of proactive and reactive inhibitory control to effectively evaluate and precisely treat MUD patients with long-term abstinence.