The emergency response process for major infectious diseases is very complex and requires synergy among multiple emergency subjects across regions, levels, and sectors to deal with the emergency response process. This study aimed to investigate the use of a complex network to construct a subject synergistic network and evaluate synergy to improve the efficiency of emergency response in cross-regional major infectious diseases. Emergency response subject synergy was identified using a “missions-resources-subjects” approach. Subject synergy was extracted from the text about cross-regional major infectious disease emergency response to construct subjects synergistic network. A synergy evaluation model was constructed and synergy was calculated by UCINET. The measurements were shown to lead to improving the efficiency of emergency response by emergency subjects synergy. This indicates that there is a possibility of improving emergency response efficiency by building a subjects synergistic mechanism and suggests that the synergy of emergency subjects needs to be transformed.