We aimed to evaluate the relationship between obesity and structural brain abnormalities assessed by magnetic resonance imaging using data from 45 observational epidemiological studies, where five articles reported prospective longitudinal results. In cross-sectional studies' analyses, the pooled weighted mean difference for total brain volume (TBV) and gray matter volume (GMV) in obese/overweight participants was -11.59 (95 % CI: -23.17 to -0.02) and -10.98 (95 % CI: -20.78 to -1.18), respectively. TBV was adversely associated with BMI and WC, GMV with BMI, and hippocampal volume with BMI, WC, and WHR. WC/WHR are associated with a risk of lacunar and white matter hyperintensity (WMH). In longitudinal studies' analyses, BMI was not statistically associated with the overall structural brain abnormalities (for continuous BMI: RR = 1.02, 95 % CI: 0.94-1.12; for categorial BMI: RR = 1.18, 95 % CI: 0.75-1.85). Small sample size of prospective longitudinal studies limited the power of its pooled estimates. A higher BMI is associated with lower brain volume while greater WC/WHR, but not BMI, is related to a risk of lacunar infarct and WMH. Future longitudinal research is needed to further elucidate the specific causal relationships and explore preventive measures.