The invention relates to a short message service (SMS) authenticated encryption system and method based on a digital certificate. The SMS authenticated encryption system comprises an SMS authentication center, an authenticated mechanism SMS center and a mobile phone. A digital certificate management service unit of the SMS authentication center provides procedures generated by the unique digital certificate of the authenticated mechanism according to the user identification, thus ensuring the safety of the digital certificate. The digital certificate is used for safety of two-way SMS communication. In the invention, the way that a plurality of different receivers respectively carry out encrypted transmission according to own keys based on the SMS numbers can be realized by only installing an SMS authentication and encryption procedure in the common mobile phone as the SMS authentication and encryption client. The invention can authenticate the received SMS contents, ensure the sent contents not to be falsified and ensure the authenticity of the senders, has good confidentiality, changes less existing SMS systems, occupies less resources, is easy to realize and can be applied to such fields as financial transactions, etc.