Background In China, medical staff of children's hospitals are commonly exposed to violence. However, few studies on medical violence are conducted in the settings of children's hospitals. The aim of this study is to assess the incidence, magnitude, consequences, and potential risk factors of workplace violence (WPV) against medical staff of children's hospitals. Methods A retrospective cross-sectional design was used. A self-administered questionnaire was utilized to collect data on 12 children's hospitals. The questionnaires were distributed to a stratified proportional random sample of 2,400 medical staff; 1,932 valid questionnaires were collected. A chi-square test and multiple logistic regression analysis were conducted. Results A total of 68.6% of respondents had experienced at least one WPV incident involving non-physical and/or physical violence in the past year. The perpetrators were mainly family members of patients (94.9%). Most of the WPV occurred during the day shift (70.7%) and in wards (41.8%). Males were 1.979 times (95% CI, 1.378 to 2.841) more likely than females to experience physical violence. Emergency departments were more exposed to physical violence than other departments. Oncology was 2.733 times (95% CI, 1.126 to 6.633) more exposed to non-physical violence than the emergency department. As a result of WPV, victims felt aggrieved and angry, work enthusiasm declined, and work efficiency was reduced. However, only 5.6% of the victims received psychological counseling. Conclusion Medical staff are at high risk of violence in China's children's hospitals. Hospital administrators and related departments should pay attention to the consequences of these incidents. There is a need for preventive measures to protect medical staff and provide a safer workplace environment. Our results can provide reference information for intervention strategies and safety measures.