Hierarchical functional structure plays a crucial role in brain function. We aimed to investigate how aging affects hierarchical functional structure and to evaluate the relationship between such effects and molecular, microvascular, and cognitive features. We used resting-state functional magnetic resonance imaging (fMRI) data from 95 older adults (66.94 ± 7.23 years) and 44 younger adults (21.8 ± 2.53 years) and employed an innovative graph-theory-based analysis (stepwise functional connectivity (SFC)) to reveal the effects of aging on hierarchical functional structure in the brain. In the older group, an SFC pattern converged on the primary sensory-motor network (PSN) rather than the default mode network (DMN). Moreover, SFC decreased in the DMN and increased in the PSN at longer link-steps in aging, indicating a reconfiguration of brain hub systems during aging. Subsequent correlation analyses were performed between SFC values and molecular, microvascular features, and behavioral performance. Altered SFC patterns were associated with dopamine and serotonin, suggesting that altered hierarchical functional structure in aging is linked to the molecular fundament with dopamine and serotonin. Furthermore, increased SFC in the PSN, decreased SFC in the DMN, and accelerated convergence rate were all linked to poorer microvascular features and lower executive function. Finally, a mediation analysis among SFC features, microvascular features, and behavioral performance indicated that the microvascular state may influence executive function through SFC features, highlighting the interactive effects of SFC features and microvascular state on cognition.