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Objective To determine whether subclinical brain dysfunction in SLE can be detected by disrupted interhemispheric connectivity and assess its modulation by immunosuppressive regimens.Methods 234 subjects (140 patients with SLE and 94 healthy controls (HCs)) were included. Through stratified analysis, patients with SLE were divided into treatment-naïve group (n=22), glucocorticoid monotherapy group (GC group, n=30) and GC combined with cyclophosphamide (CTX) and/or hydroxychloroquine (HCQ) treatment group (n=50) to assess the differences in voxel-mirrored homotopic connectivity (VMHC) between groups.Results SLE group showed lower VMHC than the HC group in bilateral superior temporal gyrus, medial superior frontal gyrus, calcarine fissure and surrounding cortex and middle occipital cortices (Gaussian random field corrected: voxel p<0.005, cluster p<0.01). The VMHC in the bilateral superior temporal gyrus (r s=−0.250, p=0.024) and medial superior frontal gyrus (rs=−0.246, p=0.026) was negatively correlated with the depression score, while the VMHC in the medial superior frontal gyrus was negatively correlated with the anxiety score (rs=−0.239, p=0.031). Three SLE subgroups and HCs had different VMHC in the postcentral/precentral gyrus (F=8.942) and anterior cingulate/paracingulate gyrus (F=9.868). Post hoc analysis found that compared with the HC group, VMHC in the treatment-naïve group was decreased in the bilateral posterior central gyrus (t=−2.953), while in the GC monotherapy group, it decreased in the posterior central gyrus (t=−2.999) and anterior cingulate/paracingulate gyrus (t=−2.999). Compared with GC combined with CTX and/or HCQ group, VMHC in GC monotherapy group was decreased in the postcentral gyrus (t=−2.999).Conclusion Even without overt neuropsychiatric symptoms, patients with SLE exhibit impaired interhemispheric functional synergy that is partially reversed by combination immunosuppression, suggesting an early targetable brain pathway.