Stroke is recognized as a network communication disorder. Advances in neuroimaging technologies have enhanced our comprehension of dynamic cerebral alterations. However, abnormal and adaptive brain activity patterns after stroke are still underexplored. We aim to identify dynamic patterns of network remodeling in stroke patients with hemiplegia. fMRI data were obtained from 50 stroke patients and 35 healthy controls to establish a spatiotemporal multilayer modularity model. Then, graph-theoretic measures, including modularity, flexibility, cohesion and disjointedness were calculated to quantify dynamic reconfiguration. Our findings reveal that the post-stroke brain exhibited higher modular organization, as well as heightened flexibility and disjointedness compared to HCs; specifically, increased flexibility and disjointedness, were observed in the Sensorimotor network, Default mode network, and Attentional network, indicating that brain nodes tend to switch more frequently and independently between communities, and the dynamic changes were mainly driven by motor control and cognition-related networks. Notably, modified functional dynamics positively correlated with better motor performance in patients with mild motor impairment. Collectively, our research uncovered high modularity, global hyper-flexibility, and independent reorganization following stroke. Our findings may offer new insights into the complex reorganization of neural function in post-stroke brain.