Glymphatic system function has been increasingly linked to cognition in cerebral small vessel disease (CSVD), although the underlying pathological mechanisms related to brain metabolism remain to be fully clarified. Iron overload within white matter hyperintensity (WMH), potentially reflecting metabolic abnormalities, may play a pivotal role in this process. This study investigated whether WMH iron burden mediates the association between glymphatic dysfunction and cognitive impairment in CSVD. A total of 102 patients with CSVD and 29 matched healthy controls (HCs) underwent brain MRI and cognitive assessments. WMH iron burden was quantified using a sub-voxel quantitative approach, while glymphatic function was assessed with the Diffusion Tensor Image Analysis aLong the Perivascular Space (DTI-ALPS) index. Correlation and mediation analyses were then conducted to evaluate relationships among WMH iron burden, DTI-ALPS index, and cognitive scores. Compared with HCs, CSVD patients exhibited significantly higher WMH iron burden, lower DTI-ALPS index, and poorer cognitive performances. Elevated WMH iron burden was associated with deficits in attention-executive (att-exe), memory, and visual-spatial domains, whereas reduced DTI-ALPS index correlated with impaired att-exe and memory function. Importantly, WMH iron burden fully mediated the link between DTI-ALPS index and both att-exe function (p < 0.001) and memory (p = 0.02) in the CSVD group. These findings noninvasively identify WMH iron overload, a probable representative of microglial activation, as a key mediator between glymphatic dysfunction and cognitive decline in CSVD, prompting a potential therapeutic target for disease management.