Background <p>Primary Sjögren’s syndrome (pSS) manifests a spectrum of neuropsychological symptoms, primarily cognitive impairment, but the mechanism of central nervous system damage remains unclear. This study sought to analyze differences in the static and dynamic fractional amplitude of low-frequency fluctuation (fALFF) and region homogeneity (ReHo) between pSS patients and healthy controls (HCs), aiming to elucidate regional brain function alterations and investigate underlying mechanisms.</p> Methods <p>Using stringent inclusion and exclusion criteria, 68 pSS patients and 69 HCs were assessed, including rs-fMRI, neuropsychological assessments, and laboratory tests. Static fALFF (sfALFF), static ReHo (sReHo), dynamic fALFF (dfALFF), and dynamic ReHo (dReHo) were calculated separately using two-sample <i>t</i>-tests to identify differences in brain regions between the two groups. Correlations between these regions and disease duration, laboratory indicators, and neuropsychological test scores were also examined.</p> Results <p>Static index analysis revealed increased sfALFF in the right supplementary motor area in pSS patients, with significant decreases in sReHo in the left orbital media frontal gyrus, left caudate nucleus, and right precuneus lobe. Dynamic index analysis showed significant increases in dfALFF in the left supplementary motor area and dReHo in the right dorsolateral superior frontal gyrus. Furthermore, sReHo in the right precuneus lobe negatively correlated with NCT-A scores (<i>P</i> = 0.005), and dReHo in the right dorsolateral superior frontal gyrus negatively correlated with DST scores (<i>P</i> = 0.007).</p> Conclusion <p>PSS patients experience notable changes in regional brain function, as evidenced by alterations in both static and dynamic brain indicators. Integrating these metrics provides a holistic view of the brain function alterations in pSS patients.</p>