With the rapid growth of railways in China, the focus has changed to the maintenance of large-scale rail structures. Multi-agent systems (MASs) based on wireless sensor network (WSNs) with soft multi-functional sensors (SMFS) are adopted cooperatively for the structural health monitoring of large-scale rail structures. An MAS framework with three layers, namely the sensing data acquisition layer, sensor data processing layer, and application layer, is built here for collaborative data collection and processing for a rail structure. WSN nodes with strain, temperature, and piezoelectric sensor units are developed for the continuous structural health monitoring of the rail structure. The feature data at different levels are extracted for the online monitoring of the rail structure. Experiments carried out at the Rail Transmit Base at East China Jiaotong University verify that the WSN nodes with SMFS are successfully assembled onto a 100-m-long track for damage detection. Based on the sensing data and feature data, a neural network data fusion agent (DFA) is applied to calculate the damage index value of the track for comprehensive decisions regarding rail damage. The use of WSNs with multi-functional sensors and intelligent algorithms is recommended for cooperative structural health monitoring in railways.