In order to improve the encryption effect and ensure the security of the data set, this study designs a privacy data set homomorphic encryption method based on the improved Rivest Shamir Adleman(RSA) algorithm. Based on the analysis of the operating principle of traditional RSA algorithm, the parameter selection and the prime number judgment condition, the improved RSA algorithm is proposed. In order to further improve the encryption speed, Data Encryption Standard(DES) algorithm is introduced. Firstly, DES algorithm is utilized to encrypt the plaintext data set, and RSA encryption is carried out for the key. On this basis, in the plaintext and ciphertext spaces, the addition homomorphism process is adopted to calculate the ciphertext, and the corresponding plaintext calculation result is obtained by decrypting the result. Experimental results show that, compared with the encryption method based on traditional RSA algorithm or DES algorithm, this method has higher encryption efficiency and higher success rate of resisting attacks. The encryption process takes time between 5 and 6?s, and the success rate of resisting attacks is kept around 95%, indicating that this method can effectively provide support for the security protection of private data sets.