Network architectural is indispensable for a wide-area and robust Fiber-optic time transfer (FOTT) network, however, there is currently a deficiency in effective scheme. This article proposed a reconfigurable FOTT network architecture based on software-defined time transfer units (SD-TTU), enhancing the network’s capability for flexible resource allocation, automatic protection and restoration. The architecture consists of three layers: 1) time transfer layer for time signal transmission and clock difference cancellation; 2) monitor and control layer for monitoring network states, fault detection, and dynamic reconfiguration of the SD-TTU; and 3) service and configuration layer for customizable service construction and proactive network reconfiguration. A polymorphic software-defined time transfer unit (SD-TTU) is further designed, which can operate as a master station, intermediate station, and slave station using the same hardware. The proposed architecture and the designed SD-TTU are experimentally demonstrated over chained and ring networks, respectively. Network expansion, contraction, topology reconfiguration, failure and fault recovery are validated. The changes of measured mean clock differences are below 43-ps across different scenarios, verifying the robustness and flexibility of the proposed architecture.