iOS Short Message Service (SMS) transmits messages in plaintext, which would lead to potential security threats of data. It is meaningful to design a safe and effective SMS. In this paper, all iOS Security Guides are referred to and all the cryptographic algorithms in iOS data protection are analyzed. Because there is no homomorphic encryption, a library of homomorphic encryption algorithms for iOS based on RSA and Paillier is developed. Using this library, a protection scheme PS-HOMO for protecting iOS SMS data is proposed and implemented. Under the premise of ensuring the data confidentiality, PS-HOMO also has the function of ciphertext operation due to the multiplicative homomorphism of RSA and additive homomorphism of Paillier. A comprehensive performance test was performed on PS-HOMO. The results show that the performance is in line with our expectations and will not have a major impact on the original system. The security of PS-HOMO is theoretically analyzed from man-in-the-middle attack, replay attack, and traffic analysis attack. Two application scenarios of the PS-HOMO, remote anonymous voting and privacy telemedicine service are envisaged. We hope PS-HOMO would play a significant role in privacy protection.