BackgroundBrain–computer interface (BCI) has been widely used for functional recovery after stroke. Understanding the brain mechanisms following BCI intervention to optimize BCI strategies is crucial for the benefit of stroke patients.MethodsForty-six patients with upper limb motor dysfunction after stroke were recruited and randomly divided into the control group or the BCI group. The primary outcome was measured by the assessment of Fugl–Meyer Assessment of Upper Extremity (FMA-UE). Meanwhile, we performed resting-state functional magnetic resonance imaging (rs-fMRI) in all patients, followed by independent component analysis (ICA) to identify functionally connected brain networks. Finally, we assessed the topological efficiency of both groups using graph-theoretic analysis in these brain subnetworks.ResultsThe FMA-UE score of the BCI group was significantly higher than that of the control group after treatment (p= 0.035). From the network topology analysis, we first identified seven subnetworks from the rs-fMRI data. In the following analysis of subnetwork properties, small-world properties includingγ(p= 0.035) andσ(p= 0.031) within the visual network (VN) decreased in the BCI group. For the analysis of the dorsal attention network (DAN), significant differences were found in assortativity (p= 0.045) between the groups. Additionally, the improvement in FMA-UE was positively correlated with the assortativity of the dorsal attention network (R= 0.498,p= 0.011).ConclusionBrain–computer interface can promote the recovery of upper limbs after stroke by regulating VN and DAN. The correlation trend of weak intensity proves that functional recovery in stroke patients is likely to be related to the brain’s visuospatial processing ability, which can be used to optimize BCI strategies.Clinical Trial RegistrationThe trial is registered in the Chinese Clinical Trial Registry, number ChiCTR2000034848. Registered 21 July 2020.