A data protection method and system thereof used for a smart card, wherein, the user may select a data frame in a smart card through a data access interface, and input data into the data frame. The data protection system includes a data protection module, an encryption-decryption module, and a data storage module. The data protection module is coupled respectively to a data access interface and a smart card. The encryption-decryption module is coupled to the data protection module, and is used to generate an encrypted data frame and a fake data frame. The data protection module is used to store the fake data frame into a smart card. When it is desired to access the data frame, the data access interface is used to read out the corresponding fake data frame.