A secrecy system and a decryption method of on-chip data stream of nonvolatile FPGA are provided in the present invention. The nonvolatile memory module of the system is configured to only allow the full erase operation. After the full erase operation is finished, the nonvolatile memory module gets into the initial state. Only the operation to the nonvolatile memory module under the initial state is effective, and thereby the encryption region unit is arranged in the nonvolatile memory module. Only the decryption data written into the encryption region unit under the initial state can make the nonvolatile memory module to be readable, so that the decryption of the system is finished, which greatly improves the secrecy precision.