This cross-sectional study aimed to describe the characteristics of physical activity-related injury (PARI) and to explore its associated factors among university students in Chaoshan district. Selected from the baseline survey in March and April, 434 students graded 1-3 from two universities were interviewed face-to-face in April and May 2017. Socio-demographics, physical activity (PA) participation, risk-taking behaviors, and PARI occurrences in the past 12 months were collected. Group Lasso logistic regression was applied to identify the risk factors of PARI. Totally, 317 PARI episodes were reported by 184 subjects with an overall injury risk of 0.73 injuries/student/year (males: 1.00, females: 0.63) and an injury incidence density of 0.81 injuries per 1000 PA exposure hours (males: 1.13, females: 0.69). Most injuries involved the lower extremities and were sprains and strains. Males, sports team members, and those with high-risk rebellious and anti-social behaviors were more likely to sustain PARI compared to their counterparts. Those who participated in vigorous-intensity PA with longer duration (particularly ≥ 150 min/week) were at a higher risk for PARI. This study indicates that PARI is a health concern among university students and great efforts should be taken to prevent them from PARI when promoting a physically active lifestyle.