According to the distributed feature of cloud computing, a parallel homomorphic encryption scheme based on the MapReduce Hadoop was proposed with the combination of homomorphic encryption and MapReduce parallel framework under Hadoop environment. The concrete parallel homomorphic encrypting algorithm was implemented, and the theoretical analysis was given to prove the security and correctness of the proposed algorithm. The evaluation experiments on the cloud cluster consisting of 4 computing nodes with total 16 Central Processing Units (CPUs) show that the data encryption of the parallel homomorphic encryption algorithm can reach the speed-up radio of 13. The experimental result shows that the proposed algorithm can reduce the time cost of data encryption and can be applied to real-time applications.