The invention discloses a software defined network controller system in named data networking and a method thereof. A control plane and a data plane of the named data networking are separated by the system. The software defined network controller system comprises a storage module which is used for storing the data plane and maintaining four data structures of the data plane including a topological structure, a rule table, a push table and a routing table, wherein the control plane utilizes the data structures to control forwarding of data flow in the named data networking; a communication module which utilizes a customized communication format to establish connection between a software defined network controller of the control plane and network equipment of the data plane, maintain connection and receive and process data flow transmitted by the named data networking; and a function module API which is used for packaging functions of the storage module and is utilized to operate the storage module by an application layer so that direction of data flow is controlled.