Transcranial alternating current stimulation (tACS) has emerged as a promising technique to non-invasively modulate the endogenous oscillations in the human brain. Despite its clinical potential to be applied in routine rehabilitation therapies, the underlying modulation mechanism has not been thoroughly understood, especially for patients with neurological disorders, including stroke. In this study, we aimed to investigate the frequency-specific stimulation effect of tACS in chronic stroke. Thirteen chronic stroke patients underwent tACS intervention, while resting-state functional magnetic resonance imaging (fMRI) data were collected under various frequencies (sham, 10 Hz and 20 Hz). The graph theoretical analysis indicated that 20 Hz tACS might facilitate local segregation in motor-related regions and global integration at the whole-brain level. However, 10 Hz was only observed to increase the segregation from whole-brain level. Additionally, it is also observed that, for the network in motor-related regions, the nodal clustering characteristic was decreased after 10 Hz tACS, but increased after 20 Hz tACS . Taken together, our results suggested that tACS in various frequencies might induce heterogeneous modulation effects in lesioned brains. Specifically, 20 Hz tACS might induce more modulation effects, especially in motor-related regions, and they have the potential to be applied in rehabilitation therapies to facilitate neuromodulation. Our findings might shed light on the mechanism of neural responses to tACS and facilitate effectively designing stimulation protocols with tACS in stroke in the future.