Knowledge gaps that limit the development of therapies for polycystic ovary syndrome (PCOS) concern various environmental factors that impact clinical characteristics. Circadian dysrhythmia contributes to glycometabolic and reproductive hallmarks of PCOS. Here, we illustrated the amelioration ofLimosilactobacillus reuteri(L. reuteri) on biorhythm disorder-ignited dyslipidemia of PCOS via a microbiota-metabolite-liver axis. A rat model of long-term (8 weeks) darkness treatment was used to mimic circadian dysrhythmia-induced PCOS. Hepatic transcriptomics certified by in vitro experiments demonstrated that increased hepatic galanin receptor 1 (GALR1) due to darkness exposure functioned as a critical upstream factor in the phosphoinositide 3-kinase (PI3K)/protein kinase B pathway to suppress nuclear receptors subfamily 1, group D, member 1 (NR1D1) and promoted sterol regulatory element binding protein 1 (SREBP1), inducing lipid accumulation in the liver. Further investigations figured out a restructured microbiome-metabolome network followingL. reuteriadministration to protect darkness rats against dyslipidemia. Notably,L. reuteriintervention resulted in the decrease ofClostridium sensu stricto 1andRuminococcaceae UCG-010as well as gut microbiota-derived metabolite capric acid, which could further inhibit GALR1-NR1D1-SREBP1 pathway in the liver. In addition, GALR antagonist M40 reproduced similar ameliorative effects asL. reuterito protect against dyslipidemia. While exogenous treatment of capric acid restrained the protective effects ofL. reuteriin circadian disruption-induced PCOS through inhibiting GALR1-dependent hepatic lipid metabolism. These findings purport thatL. reutericould serve for circadian disruption-associated dyslipidemia. Manipulation ofL. reuteri–capric acid–GALR1 axis paves way for clinical therapeutic strategies to prevent biorhythm disorder-ignited dyslipidemia in PCOS women.