From 68 studies including 5407 patients (MS: 2368; NMOSD: 2369; MOGAD: 670), pairwise analysis showed MS had greater volume loss in white matter, cerebellum, brainstem, and deep grey matter structures (thalamus, caudate, putamen, pallidus, amygdala, accumbens) compared to NMOSD, but not MOGAD. MS demonstrated higher T2 lesion volume than NMOSD (SMD=1.03, p=0.0003) and MOGAD (SMD=0.62, p=0.01). NMOSD showed more pronounced whole brain and grey matter loss than MOGAD (SMD=-0.39, p=0.0002; SMD=-0.40, p=0.0004). NMA rankings indicated MS worst for global brain volume, deep grey matter, and lesion volumes; MOGAD displayed intermediate reductions across structures. Results were consistent across sensitivity analyses without major inconsistency.