Background:The competencies of medical staff in the public health emergency system and evaluated the effects of system-based professional training were investigated. Material and Methods: A competency model for individuals in a public health emergency management system was developed, which contained 33 items with 5 domains. A competency-based intervention was performed. A total of 68 participants from 4 health emergency teams in Xinjiang, China were recruited and randomly divided into 2 groups: the intervention (N = 38) and control groups (N = 30). Participants in the intervention group received competency-based training, while those in the control group received no training. All participants responded to the COVID-19 activities. The competencies of medical staff in the 5 domains were then analyzed in the pre-intervention, post-first training, and post-COVID-19 intervention using a self-designed questionnaire. Results: Participants' competencies were at the middle level at baseline. After the first training, competencies in the 5 domains significantly improved in the intervention group; in the control group, there was a significant increase in professional quality compared in the pre-training. After the response to COVID-19, the mean scores of competencies in the 5 domains significantly increased in both the intervention and control groups compared with those in the post-first training. Psychological resilience scores were higher in the intervention group than in the control group, whereas no significant differences in competencies were found in other domains. Conclusions: Competency-based interventions provided practice and showed a positive effect on improving the competencies of medical staff in public health teams.