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This review systematically explores the circadian system and constructs an integrated framework linking disruption to the synergistic dysregulation of multiple pathways and subsequent emotional\/sleep abnormalities. We systematically examine five key mechanistic pathways: the SCN-limbic circuit, HPA axis, immune inflammation, neurotransmitter plasticity, and the gut-brain axis. Furthermore, we define actionable subtypes of disruption, summarize chronotherapies (e.g., light therapy, melatonin), and analyze current controversies regarding causality. Finally, we propose future directions, including multi-omics sampling and personalized intervention algorithms. By integrating evidence linking circadian disruption to anxiety\/depression, this paper highlights its central mechanistic value, providing theoretical support for precision psychiatry and the integration of circadian medicine.<\/jats:p>","DOI":"10.3389\/fpsyt.2026.1842599","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T10:42:37Z","timestamp":1785926557000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["When the biological clock is disordered: circadian rhythm disruption as a core pathophysiological mechanism in anxiety and depression"],"prefix":"10.3389","volume":"17","author":[{"given":"Jiao","family":"Yuan","sequence":"first","affiliation":[{"name":"Department of Psychology, Ward 1, Qingdao Mental Health Center","place":["Qingdao, 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