Cyber physical system (CPS) is facing enormous security challenges because of open and interconnected network and the interaction between cyber components and physical components, the development of cyber physical systems is constrained by security and privacy threats. A feasible solution is to combine the fully homomorphic encryption (FHE) technique to realize the efficient operation of ciphertext without decryption. However, most current homomorphic encryption algorithms only support limited data types, making it difficult to be widely applied in actual environment. To address this limitation, we propose a parallel fully homomorphic encryption algorithm that supports floating-point numbers. The proposed algorithm not only expands the data types supported by the existing fully homomorphic encryption algorithms, but also utilizes the characteristics of multi-nodes in cloud environment to conduct parallel encryption through simultaneous group-wise ciphertext computations. The experimental results show that, in a 16-core 4-node cluster with MapReduce environment, the proposed encryption algorithm achieves the maximum speed-up exceeding 5, which not only solves the limited application problem of the existing fully homomorphic encryption algorithm, but also meets the requirements for the efficient homomorphic encryption of floating-point numbers in cloud computing environment. © 2019, The Author(s).