The invention provides an electromagnetic tomography nondestructive inspection device for severe fault of a rail and a method thereof. The inspection device comprises an L-shaped array sensor, an electromagnetic tomography nondestructive inspection case, a fault detection monitoring and recording computer and a fault detection monitoring liquid crystal panel, wherein the electromagnetic tomography nondestructive inspection case comprises a power driving circuit, an excitation direction control circuit, an excitation current distribution VCCS array, an excitation signal distribution amplification circuit, an orthogonal program control two-channel DDS excitation signal generator, a bus, a system power supply, an FPGA synchronous control circuit, a preposed signal conditioning circuit, a signal digital demodulation FPGA chip, an embedded system, a communication interface and a liquid crystal display module. The device and the method can ensure on-line inspection of rail fault inspection along with train operation, and is convenient for discovering the condition of serious fault of the rail with severe potential danger to rail transportation in time.