A communication system and method for protecting messages between two mobile phones are provided. The method sets protective parameters in a first mobile phone, generates an encryption key and a decryption key according to the protective parameters, stores the decryption key into a storage device of the first mobile phone, and registers the encryption key to a second mobile phone through a wireless network. The method further encrypts a short message into an encrypted message in the second mobile phone according to the encryption key, and sends the encrypted message to the first mobile phone through the wireless network. In addition, the method decrypts the encrypted message to a readable message when the first mobile phone receives the encrypted message, and displays the readable message on a display screen of the first mobile phone.