Integrated with cloud computing technologies, a large-scale cyber-physical system (CPS) can outsource its extensive computations to a cloud, creating a cloud-enabled CPS (CE-CPS). However, outsourcing the computation to an untrusted cloud may expose the privacy of the data in the CPS. To this end, this paper presents a secure and practical mechanism to securely outsource the output feedback control problem of a large-scale CPS. Our approach combines a standard homomorphic encryption (SHE) and a customized homomorphic encryption (CHE), allowing the cloud to process computation on the ciphertexts and return the desired results. We analyze the correctness and security of the proposed mechanism. We also investigate the performance and stability of CPS under the quantization errors caused by encryption. In the end, we use experiments to evaluate the performance of the mechanism.