Most of China's top hospitals in 19 major medical specialties are in Beijing, Shanghai and Guangzhou, according to the China National Medical Information Center.
The research is based on data collected from 48 million clinical cases in nearly 400 level-three (top level) public hospitals nationwide between 2006 and 2014.
Analysis of cases contributed 70 percent of ranking points while the remainder are awarded based on interviews with medical professionals supported by an independent research organization.
The 19 specialties are those to have received the greatest number of patients, such as obstetrics, gynecology, pediatrics and stomatology.
Peking Union Medical College Hospital is among the top three hospitals in nine medical specialties, including endocrinology, general surgery, obstetrics and gynecology.
"Without the concerns of academic reputations the results are based on factors closely related to medical services and treatment," said Ao Yingfang, party secretary of Peking University Health Science Center.
According to Ao, major factors in the evaluation included the mortality rate after surgery, average days of hospital stay and postoperative complication rate.
Zhao Minggang, director of the National Center of Hospital Administration, said the center will collect more information in future and support health policy-making and surveillance of quality control and treatment.
The information center, under the National Health and Family Planning Commission, was formally named the Medical Information Center at Peking University Health Science Center, established in 2010.