This study models the abnormal workflow in hospitals by extending the components of polychromatic sets and polychromatic graph. First, the research progress of abnormal workflows is introduced. Second, the theories needed for formalization of this study—polychromatic sets and polychromatic graph are described. According to the particularity of the research object, the components in the polychromatic sets are expanded to construct personal colors and the enclosure matrix of the volume represents the relationship between anomalous events and anomaly types. The enclosure matrix of edges and objects has been added to the polychromatic diagram to describe the starting point and ending point of the arc of abnormal handling behavior, constructed an hospital abnormal workflow processing model based on polychromatic graph. Finally, the hospital outpatient registration process exception handling is used as an example to verify the correctness of the model.