The present invention discloses a comprehensive management system for health certificates which integrates the Internet of things, cloud computing, Beidou positioning, biological recognition and the like technologies. The system comprises: a cloud computing center, a PC terminal, an information acquisition terminal and an enforcement terminal. According to the present invention, the Beidou positioning technology is firstly applied in the field of health certificate management, the biological recognition technology is firstly applied in the field of health certificate management, the Internet of things technology is firstly applied in the field of heath certificates, and the Internet of things, cloud computing, Beidou positioning and biological recognition are organically integrated. By using the network-based big data information management technology, data information of the health certificates is stored, processed and published, which not only saving man power and resources, but also greatly improves the efficiency. In addition, the errors caused by man-made neglects can be reduced, and person-to-certificate mapping is achieved. According to the present invention, the health certificates are authenticated onsite over the Internet, thereby simply recognizing the false certificates and improving the working efficiency.