Disruption of brain resting-state networks (RSNs) is known to be related to stroke exposure, but determining causality can be difficult in epidemiological studies. We used data on genetic variants associated with the levels of functional (FC) and structural connectivity (SC) within 7 RSNs identified from a genome-wide association study (GWAS) meta-analysis among 24,336 European ancestries. The data for stroke and its subtypes were obtained from the MEGASTROKE consortium, including up to 520,000 participants. We conducted a two-sample bidirectional Mendelian randomization (MR) study to investigate the causality relationship between FC and SC within 7 RSNs and stroke and its subtypes. The results showed that lower global mean FC and limbic network FC were associated with a higher risk of any ischemic stroke and small vessel stroke separately. Moreover, ventral attention network FC and default mode network SC have a positive causal relationship with the risk of small vessel stroke and large artery stroke, respectively. In the inverse MR analysis, any stroke and large artery stroke were causally related to dorsal attention network FC and somatomotor FC, respectively. The present study provides genetic support that levels of FC or SC within different RSNs have contrasting causal effects on stroke and its subtypes. Moreover, there is a combination of injury and compensatory physiological processes in brain RSNs following a stroke. Further studies are necessary to validate our results and explain the physiological mechanisms.