This study aimed to examine the effects of chronic methamphetamine use on the topological organization of whole-brain functional connectivity network (FCN) by reconstruction of neural-activity time series at resting-state. The EEG of 36 individuals with methamphetamine use disorder (IWMUD) and 24 normal controls (NCs) were recorded, pre-processed and source-reconstructed using standardized low-resolution tomography (sLORETA). The brain FCNs of participants were constructed and between-group differences in network topological properties were investigated using graph theoretical analysis. IWMUD showed decreased characteristic path length, increased clustering coefficient and small-world index at delta and gamma frequency bands compared to NCs. Moreover, abnormal changes in inter-regional connectivity and network hubs were observed in all the frequency bands. The results suggest that the IWMUD and NCs have distinct FCNs at all the frequency bands, particularly at the delta and gamma bands, in which deviated small-world brain topology was found in IWMUD.