The invention aims at providing a network architecture security system for Internet of Things and a security method thereof, comprising security protective measures sequentially established in the system from inside to outside, which are mainly reflected in that a security device at a central terminal of the Internet of Things comprises a central cipher machine, a central authentication secret key management center, a data server, a security database and the like, and then the security of each sensor terminal in a Personal Area Network and the like. Compared with the prior art, the invention has the advantages that: 1. according to the characteristics of the Internet of Things, Internet security technology of the Internet of Things is realized; 2. the security protective measures sequentially established in the system from inside to outside are mainly reflected in the security device at the central terminal and security modules at each sensor terminal, thus ensuring the security of sensing information, equipment, communication and application, as well as security management; and 3. multi-level security systems are deployed in the aspects of security mechanism and management, such as the confidentiality, integrity, authenticity and non-repudiation of data, and equipment legitimacy.