Mental fatigue is growingly considered to be associated with functional brain dysconnectivity. Although conventional wisdom suggests that rest break is an effective countermeasure, the underlying neural mechanisms and how they modulate fatigue-related brain dysconnectivity is largely unknown. Here, we introduce an empirical method to examine the reorganization of dynamic functional connectivity (FC) in a two-session experiment where one session including a mid-task break (Rest) compared to a successive task design in the other session (No-rest). Temporal brain networks were estimated from 20 participants and the spatiotemporal architecture was examined using our newly developed temporal efficiency analysis framework. We showed that taking a mid-task break leads to a restorative effect towards the end of experiment instead of immediate post-rest behaviour benefits. More importantly, we revealed a potential neural basis of our behaviour observation: the reduced spatiotemporal global integrity of temporal brain network in No-rest session was significantly improved with the break opportunity in the last task block of Rest session. Overall, we provided novel evidence to support beneficial effect of rest breaks in both behaviour performance and brain function. Moreover, these findings extended prior static FC studies of mental fatigue and highlight that altered dynamic FC may underlie cognitive fatigue.