Methamphetamine (MA) could induce functional and structural brain alterations in dependent subjects. However, few studies have investigated resting-state activity in methamphetamine-dependent subjects (MADs). We aimed to investigate alterations of brain activity during resting-state in MADs using fractional amplitude of low-frequency fluctuation (fALFF) and regional homogeneity (ReHo). We analyzed fALFF and ReHo between MADs (n = 70) and healthy controls (HCs) (n = 84) and performed regression analysis using MA use variables. Compared to HCs, abstinent MADs showed increased fALFF and ReHo values in the bilateral striatum, decreased fALFF in the left inferior frontal gyrus, and decreased ReHo in the bilateral anterior cingulate cortex, sensorimotor cortex, and left precuneus. We also observed the fALFF values of bilateral striatum were positively correlated with the age of first MA use, and negatively correlated with the duration of MA use. The fALFF value of right striatum was also positively correlated with the duration of abstinence. The alterations of spontaneous cerebral activity in abstinent MADs may help us probe into the neurological pathophysiology underlying MA-related dysfunction and recovery. Since MADs with higher fALFF in the right striatum had shorter MA use and longer abstinence, the increased fALFF in the right striatum might implicate early recovery during abstinence.