Abstract: An intermediate code encryption method based on fully homomorphic encryption technology, and a ciphertext virtual machine system; instructions and data of an application in a virtual machine are fully homomorphically encrypted by improving a function key part, and output result ciphertext is obtained by performing ciphertext identification on input data and adopting corresponding homomorphic processing operations, so that running of the virtual machine in an encrypted environment is implemented; according to the present invention, an application is fully homomorphically encrypted, not only data in the program but also instructions of the program are encrypted, and thus, the program logic and structure are protected to the greatest extent.