Objective To explore changes in peripheral biological clock rhythms in patients with ischemic stroke and to analyze the correlation between such changes and alterations in functional connectivity in specific brain regions. Methods Using a prospective case-control design， 17 ischemic stroke patients were recruited as the stroke patient group from January 2018 to July 2019 at the Department of Neurorehabilitation， China Rehabilitation Research Center， and 17 healthy controls were recruited from the community as the healthy control group. The oscillatory periods of peripheral brain and muscle ARNT-Like protein 1（ Bmal1） expression in U2OS cells after serum treatment were compared between the two groups. Resting-state functional magnetic resonance imaging（ rs-fMRI） was used to compare changes in brain functional connectivity between the two groups with bilateral hypothalamus as seed points. Spearman correlation was used to analyze the correlation between changes in biological clock rhythms and alterations in brain functional connectivity among stroke patients. Results The peripheral Bmal1 daily oscillation period was longer in stroke patient group［ （24.33±0.42） h］ than in healthy control group［ （23.81±0.48） h］， and the difference was statistically significant（ t=3.352， P=0.002）. In terms of brain functional connectivity， stroke patient group demonstrated enhanced brain functional connectivity from the hypothalamus to the right talar gyrus and from the hypothalamus to the right Roland's insula lid， and the extent of this enhanced brain functional connectivity was positively correlated with the length of the Bmal1 oscillatory period， with statistically significant differences（ r=0.369， P=0.032； r=0.393， P=0.022）. Conclusions Peripheral biological clock rhythms are altered in patients with ischemic stroke and may be associated with changes in functional connectivity in specific brain regions.