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This review systematically examines how the integration of AI with single-cell multi-omics and spatial multi-omics advances the resolution in deciphering brain cellular architecture across health and disease states. Through systematic evaluation of multi-omics datasets from neurodegenerative, psychiatric, and neurodevelopmental disorders, we demonstrate how AI facilitates disease subtype stratification, biomarker discovery, and therapeutic target identification. We critically address translational challenges, including data standardization, model interpretability, and regulatory frameworks for clinical implementation. Notably, the establishment of the International Consortium for Primate Brain Mapping in 2025 exemplifies ongoing global collaborative efforts toward systematic multi-omics atlas construction across species and disease states. This synthesis underscores a paradigm shift toward AI-enabled, mechanism-driven analyses, ultimately positioning precision neurology as a realizable framework for individualized diagnosis and targeted interventions in complex brain disorders.\u2002<\/jats:p>","DOI":"10.1093\/gigascience\/giag075","type":"journal-article","created":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T11:23:56Z","timestamp":1782127436000},"source":"Crossref","is-referenced-by-count":1,"title":["From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-9534-0303","authenticated-orcid":false,"given":"Youzhe","family":"He","sequence":"first","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]},{"name":"BGI Research , Hangzhou 310030 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