The steam generator is one of the most essential equipment of the nuclear power device which takes part in heat exchanging. The water level system of a steam generator has the peculiarities of apparent nonlinearity, large inertia and time-delaying. Furthermore, the water level of a steam generator has a direct impact on the quality of the outlet steam and the security of the system. Thus, it is significant and necessary to maintain the water level within a safety limit. the mathematical model of the steam generator, which is difficult to be described with integer order, can be established relatively clearly and precisely by using the fractional order calculus. With the progress of the modern technology, the merits of using a fractional order model become increasingly obvious due to its good performance in describing the actual plants and the dynamic process. This paper proposes a fractional order system identification method which can identify the model parameters concisely. This method is simple to be realized and also has a good adaptability to the initial value. The proposed fractional order identification scheme provides a new method of the important equipment modeling in nuclear power plant. The model that established by this method can provide research basis and technical support of the high precision and performance index control system.