The invention discloses an identity authentication based virtual terminal safety environment protection method and system. The system comprises an intelligent storage monitoring layer, a storage serving layer, and a core safety layer, wherein the intelligent storage monitoring layer comprises a storage access redirecting module, is in charge of monitoring and analyzing data access acts of application programs, and performs actions according to configuration rules, the storage access redirecting module transfers input/output access according to access control rules, the storage serving layer is in charge of encrypting and decrypting files or data and recording file mapping relations, and the core safety layer is the basis of the whole framework, provides a key management function, provides encryption and decryption support for the storage serving layer, and dispatches different algorithms as desired. By means of the identity authentication based virtual terminal safety environment protection method and system, safety of core application data can be protected, data leakage is prevented, and data inside and outside the environment are isolated without influence and do not influence user operation habits.