Based on the physical health test data of 51 967 students at such 5 universities in Guangdong as Guangdong University of Traditional Chinese Medicine, Guangdong Medical University, Guangdong University of Petroleum and Chemical Technology, Zhaoqing University and Huizhou University in 2015, the authors probed into the physical health differences between the students of different regions, urban and rural areas and different grades by using Gini coefficient, carried out a comprehensive evaluation on the students’ physical health by applying factor analysis, and revealed the following findings: in terms of physical health difference, it was bigger between regions, smaller between urban and rural areas, the smallest between grades; in terms of physical health level, the Pearl River Delta region was higher than other regions, the urban areas was higher than the rural areas, the freshmen were lower than the sophomores, it showed a trend of declining from the sophomores to the seniors, the female students were higher the male students; the physical health differences of the university students were formed at elementary and middle school age stages before university, related to the education fairness at elementary and middle school stages of basic education.