In order to improve the control performance of a position-sensorless in a flywheel energy storage system, a flywheel motor necessarily has functions of parameter identification and parameter self-tuning. This paper provides a rotor position extension observer on the basis of online identifying an unknown parameter by means of a recursive least squares discrete identification method, such that a position observation link has relatively high robust performance. Firstly, the mathematical model of flywheel motor is established and discretized. On this basis, rotor position estimation method is adopted by introducing back EMF estimation value into the calculation of nonlinear expansion observer. Then, recursive least square identification algorithm is applied to flywheel motor discrete model and key electromagnetic parameters such as stator resistance and AC-DC axis inductance can be identified at the same time, so as to eliminate rotor position estimation error caused by flywheel motor model error and improve system position-free detection performance. Finally, a hardware experimental platform based on DSP2812 is established. Simulation and experimental results show that the mentioned algorithm has certain accuracy and a certain real-time feature for the identification of the unknown parameter, and can achieve the operation control of the position-sensorless in the flywheel energy storage system. This work is supported by National Natural Science Foundation of China (No. 51777197).