The invention discloses a multiple application protocol identification method and an application protocol identification engine. According to the multiple application protocol identification method, characteristic conditions, decryption suite conditions, application protocol characteristics, application protocol hit action, various detection identification modules and corresponding rule description methods are provided on the basis of XM language; the application protocol identification engine comprises identification modules, such as a strong correlation identification module, a single packet identification module, a multi-packet identification module, an algorithm decryption and identification module and a channel extraction and identification module; a configuration module; and an application protocol characteristic matching unit, a full-flow table storage unit, a half-flow association table storage unit, and a rule base storage unit. By the use of the multiple application protocol identification method and the application protocol identification engine, flexible rule description configuration mechanisms and online, accurate and comprehensive identification of application protocols and encrypted traffic are achieved.