Abstract: Background: Heart rate variability (HRV) as an accurate, noninvasive measure of the Autonomous Nervous System (ANS) can reflect mental health (e.g., stress, depression, or anxiety). Tai Chi and Yoga (Tai Chi/Yoga), as the most widely practiced mind–body exercises, have shown positive outcomes of mental health. To date, no systematic review regarding the long-lasting effects of Tai Chi/Yoga on HRV parameters and perceived stress has been conducted. Objective: To critically evaluate the existing literature on this topic. Methods: Five electronic databases (Web of Science, PubMed, Scopus, SportDiscus and Cochrane Library) were searched from the start of the research project to July 2018. Study selection, data extraction, and study quality assessment were independently carried out by two reviewers. The potentially identified randomized controlled trials (RCT) reported the useful quantitative data that were included only for meta-analysis. Results: meta-analysis of 17 medium-to-high quality RCTs showed significantly beneficial effects on HRV parameters (normalized low-frequency, Hedge’s g = −0.39, 95% CI −0.39 to −0.56, p < 0.001, I2 = 11.62%; normalized high-frequency, Hedge’s g = 0.37, 95% CI 0.22 to −0.52, p < 0.001, I2 = 0%; low-frequency to high-frequency ratio, Hedge’s g = −0.58, 95% CI −0.81 to −0.35, p < 0.001, I2 = 53.78%) and stress level (Hedge’s g = −0.80, 95% CI −1.17 to −0.44, p < 0.001, I2 = 68.54%). Conclusions: Stress reduction may be attributed to sympathetic-vagal balance modulated by mind–body exercises. Tai Chi/Yoga could be an alternative method for stress reduction for people who live under high stress or negative emotions.