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The information application system is secured from various aspects. The user identity authentication and access control are key points for security of the information application system. In this paper, the weak security of the conventional and single authentication is analyzed and the principle of user identity authentication and access control is analyzed and studied. Combined with the smart card PKCS11 and J2EE component technology, the dual-factor authentication system which is based on the personal identity number (PIN) authentication and the hardware USB Key digital certificate authentication is designed and realized. Based on this design and realization model, the security authentication protocol, J2EE application realization process, key signature and authentication algorithm of dual-factor authentication system are described mainly. The application result shows that the security is higher if it has the similar performance.