Heart rate variability (HRV) is related to cardiac vagal control and emotional regulation and an index for cardiac vagal control and cardiac autonomic activity. This study aimed to develop the Taiwan HRV normative database covering individuals aged 20 to 70 years and to assess its diagnosing validity in patients with major depressive disorder (MDD). A total of 311 healthy participants were in the HRV normative database and divided into five groups in 10-year age groups, and then the means and standard deviations of the HRV indices were calculated. We recruited 272 patients with MDD for cross-validation, compared their HRV indices with the normative database, and then converted them to Z-scores to explore the deviation of HRV in MDD patients from healthy groups. The results found a gradual decline in HRV indices with advancing age in the HC group, and females in the HC group exhibit higher cardiac vagal control and parasympathetic activity than males. Conversely, patients in the MDD group demonstrate lower HRV indices than those in the HC group, with their symptoms of depression and anxiety showing a negative correlation with HRV indices. The Taiwan HRV normative database has good psychometric characteristics of cross-validation.