We aim to investigate functional topological brain networks changes in cerebral small vessel disease (CSVD) patients with and without cerebral microbleeds (CMBs). We divided the subjects into three subgroups: CSVD with CMBs (CSVD-c), CSVD without CMBs (CSVD-n) and control. Then, we analyzed topological disruptions between groups using graph theory and related these alterations to clinical parameters. CSVD-c showed significantly altered global, nodal topological properties and disrupted distribution of hub regions, involving the default mode network (DMN), attention, sensorimotor and visual functional areas. These findings extended our understanding of neurobiological mechanisms of CSVD.