To date, a growing number of clinical studies have demonstrated the safety and health benefits from Baduanjin intervention. Based on this, our objective is to systematically retrieve and summarize the clinical studies on Baduanjin, with a view to providing more evidence-based evidence in support of the application of Baduanjin for healthcare, and to identify the shortcomings of existing research and provide feasibility suggest for further clinical research. Both four English language and four Chinese language electronic databases were used to search articles related to Baduanjin during 2000–2019. SPSS 22.0 software was used to analyze the data, and the risk of bias tool in the RevMan 5.3.5 software was used to evaluate the methodological quality of randomized controlled trials. A total of 810 publications were identified, including 43 (5.3%) systematic reviews, 614 (75.8%) randomized controlled trials, 66 (8.1%) nonrandomized controlled clinical studies, 84 (10.4%) case series, and 3 (0.4%) case reports. The top 10 diseases/conditions included diabetes, chronic obstructive pulmonary disease, hypertension, low back pain, neck pain, stroke, coronary heart disease, cognitive impairment, insomnia, and osteoporosis or osteopenia. The style of State General Administration of Sport of China in 2003 was the most commonly used version of Baduanjin, and Baduanjin was practiced with an average of 35 minutes, 1 or 2 times a day, 3–5 days per week, and a 18-week average duration. It is also worth noting that there were no serious adverse events related to Baduanjin intervention. Most studies were small sample size research, and the methodological quality of randomized controlled trials is generally low. The clinical studies of Baduanjin have a substantial quantity and evidence base. However, there are significant differences among different studies in the specific intervention measures such as style, intensity, duration, learning, and practice methods, which need to be further standardized and unified. Further high-quality designed and reporting studies are recommended to further validate the clinical benefits of Baduanjin.