Aims: To investigate the differences in disrupted rhythms between healthy people and patients with functional gastrointestinal disorders (FGIDs) and their associations with mood disorders during the coronavirus disease 2019 (COVID-19) pandemic. Methods: The rhythm scales were composed of subscales 1 and 2 for the assessment of life-work and entertainment rhythms, respectively; Zung's Self-Rating Anxiety Scale (SAS) and Self-Rating Depression Scale (SDS) were used to assess mood disorders. Results: A total of 671 patients with FGIDs and 4373 healthy people successfully participated. The scores of subscales 1 and 2 for patients with FGIDs were significantly higher than those for healthy people (p < .005). The SAS and SDS scores, their prevalence rates were significantly higher than those for the healthy group (all p < .001). Health status, current occupation, life-work rhythm, SDS, and SAS were independent related factors of FGIDs. The score of life-work-entertainment rhythm was significantly positively correlated with SDS and SAS (both p < .001). Conclusion: Disrupted rhythms in patients with FGIDs under the COVID-19 pandemic were more frequently and significantly positively associated with mood disorders.