Firstly, we identified significant associations between social isolation, loneliness, and the incidence of 7 neurological disorders, including dementia, AD, Parkinson's disease, stroke, multiple sclerosis, epilepsy, and sleep disorders, and 4 psychiatric disorders including schizophrenia, bipolar affective disorder, anxiety disorders, and major depressive disorder (MDD). MR analyses confirmed the relationship from loneliness to sleep disorders, schizophrenia, and MDD. Secondly, we observed significant cross-sectional associations of social isolation, loneliness and behavioral phenotypes, including worse cognition, emotion and movement, and altered brain structures, including cortical (lingual, lateral occipital, and inferior parietal cortex) and subcortical (nucleus accumbens, hippocampus, thalamus, lateral ventricle) regions, as well as white matter hyperintensities, and CSF AD pathological biomarkers, including decreased CSF Aβ42 and Aβ40 levels, and increased CSF T-tau/Aβ42 ratio. Additionally, the mediation analysis indicated that the peripheral inflammatory and biochemical markers might partially mediate the associations of social isolation, loneliness and neuropsychiatric disorders.