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Objective The characteristics of heart rate variability (HRV) in patients in the functional examination department of a Shanghai hospital from 2023 to 2024 were analyzed. Methods Ninety-five patients who received functional examination in our hospital from 2023 to 2024 were selected as the study objects, including 33 patients with depression, 32 patients with anxiety, and 30 patients with insomnia. Hrv-related indicators of patients with depression, anxiety and insomnia were compared respectively: The standard deviation (SDNN) of the difference of heartbeat cycles, the whole process is divided into consecutive periods by 5 minutes, the mean value of N-N interval every 5 minutes is calculated, then the standard deviation (SDNN5) of all the mean values are calculated, and the number of beats in all N-N interval periods where the difference between adjacent N-N interval periods is greater than 50ms is divided by the total number of NN interval periods. Finally, multiply by 100 (pNN50), the root-mean-square value (RMSSD) of the difference between all adjacent N-N intervals, extremely low frequency power (VLF), low frequency power (LF), high frequency power (HF), total power (TP), LF/HF. The HRV-related indexes of patients of different genders and ages were compared respectively: SDNN, SDNN5, pNN50, RMSSD, VLF, LF, HF, TP, LF/HF. Results There was no significant difference in the levels of SDNN, SDNN5, pNN50, RMSSD, VLF, LF, HF, TP and LF/HF in patients with depression, anxiety and insomnia (P > 0.05). There was no significant difference in SDNN, SDNN5, pNN50, RMSSD, VLF, LF and TP between male and female patients (P > 0.05). There were significant differences in HF and LF/HF levels between male and female patients (P < 0.05). There were significant differences in the levels of SDNN, SDNN5, VLF, LF, TP and LF/HF among different age groups (P < 0.05). There was no significant difference in pNN50, RMSSD and HF levels among different age groups (P > 0.05). Conclusion HRV has a certain predictive power for patients with depression, anxiety and insomnia in the functional examination department of a Shanghai hospital from 2023 to 2024. In addition, the HF and LF/HF levels of HRV related indicators may be correlated with gender. At the same time, with the increase of age, the levels of SDNN, SDNN5, VLF, LF, TP, LF/HF showed a decreasing trend, and the autonomic nervous system function of the body was also declining.