Significant differences in salivary microbiota communities between polycystic ovary syndrome (PCOS) patients and healthy controls have been reported, and interestingly, some salivary microbiota exhibit diurnal oscillation in healthy people. However, whether the diurnal oscillation of salivary microbiota is present in PCOS patients is unknown. In this study, we describe the differences in the saliva microbiome between the PCOS group and the control group at different time points over 24 h. 16S rRNA gene amplicon sequencing was performed on salivary and fecal samples from 10 PCOS patients and 10 healthy controls, and salivary samples were collected at 6-h intervals over 24 h (Zeitgeber (ZT)0, ZT6, ZT12, and ZT18). Among the salivary samples, those from the PCOS group showed significant differences from those of the control group at each time point. Differences were evident in taxa level and metabolic pathways. Interestingly, we found that PCOS disrupted the diurnal rhythm of the salivary microbiota abundance, as determined in the group of healthy women. In addition, no similar changes were found in PCOS patients and controls between the oral and fecal microbiota, including differential microbiota at the phylum level. In this study, significant differences in the composition of the salivary microbiota between PCOS and healthy women were detected at different time points. We also showed that the diurnal rhythm of relative abundance of the salivary microbiota was disrupted in patients with PCOS, which might be related to development of oral-related diseases and systematic metabolic disorders.