The invention discloses a system combined with smartphones of carrying out digital signature and certification, file encryption and decryption by utilizing mobile key technology, which saves user keys or certificates on the smartphones and also carries out the processes of signature/ certification, encryption/decryption on the smartphones. The invention mainly uses a smartphone of Windows mobile operating system, a desktop computer software module and a smartphone software module. Firstly, a mobile key client is designed and realized on the desktop computer, including file encryption and decryption files, office signature, and certification Plug-ins. Then, a security system of mathematical manipulation of digital signature, certification, file encryption/decryption, etc. is designed and realized on the smartphone. Beside the inherent advantages of a USB key of convenient use, high security, etc., the invention also has multiple advantages that the USB Key does not have, such as, rapid arithmetic speed, long key support, supporting the processing of overlarge files, good sharing performance, high security and better expandability.