With the rapid development of rail transit system, it is becoming more demanding for structural health monitoring (SHM) of the train. It is crucial to supply power for sensing devices on the freight wagon to ensure the safe operation of rail transit systems. Three-mode nonlinear hybrid piezoelectric-electromagnetic vibration energy harvester (TNHVEH) with a three-layer pickup system has been designed and applied to efficiently harvest vibration energy on the axle box of freight wagons for providing the power of the sensors for online SHM. Dynamic coupling model of the vehicle-harvester system is built to devote the relationship between the operation bandwidth and the nonlinear degree of TNHVEH for broadening the operation frequency band. Simulation and experimental results demonstrate that the resonant frequencies of the three pickup systems of TNHVEH are concentrated around 27, 70, and 120 Hz, matching the representative frequencies of axle box vibrations. A maximum output voltage of 2.97 V and output power of 29.4 μW under an optimal load of 300 kΩ at 0.5 g acceleration is achieved. It successfully lights up 53 LEDs with “ECJTU” patterns, providing a solution to the power supply problem of microelectronic devices on freight wagons.