A software protection method includes decrypting an encrypted executable file by a processor, and the steps of decrypting include the following steps. A linking instruction is executed in a first execution environment; based on the linking instruction, a signature corresponding to the encrypted executable file is generated in the first execution environment; based on the signature and a hash table, a decryption algorithm is performed and a key is generated in the first execution environment; and the key is transmitted from the first execution environment to a second execution environment that is different from the first execution environment. The encrypted executable file is in the second execution environment. A software protection system is also disclosed herein.