A hierarchical fault classification method for a fuel cell system, a multi-stage fault diagnosis method therefor, and a fault diagnosis device therefor are disclosed. The fuel cell system is divided into a subsystem, a component, and an element step by step. The multi-stage fault diagnosis method includes detecting a subsystem, a fault of which occurs, in the fuel cell system composed of a plurality of subsystems and detecting an upper-level component, which causes the fault, among upper-level components included in the subsystem, the fault of which occurs, using measurement data and a control signal.