Many studies have reported meditation training has beneficial effects on brain structure and function. However, very little is known about meditation-induced changes in brain complex networks. We used network analysis of electroencephalography theta activity data at rest before and after 1-week of integrative body–mind training (IBMT) and relaxation training. The results demonstrated the IBMT group (but not the relaxation group) exhibited significantly smaller average path length and larger clustering coefficient of the entire network and two midline electrode nodes (Fz and Pz) after training, indicating enhanced capacity of local specialization and global information integration in the brain. The findings provide the evidence for meditation-induced network plasticity and suggest that IBMT might be helpful for alterations in brain networks.