The generation of the multi-key-pair in the RSA iterative encryption system was studied, and from the generation algorithm of key, a sort of multi-key-pair generation scheme was proposed in the article. In the scheme, the encryption key set and the decryption key set used in the encryption system were managed by the improved half-generation algorithm, and the management scheme that one secrete key was used to generate multiple key pairs could solve the difficult management problem for multiple key sets. Finally, the key generation algorithm was simulated by VB6.0 in the article.