The precise model of the fine tracking system (FTS) provides a crucial condition to study the control strategy, and find the key factors which impact the dynamic and static characteristics of FTS. The fine tracking identify system is designed in this paper which includes the fast steering mirror (FSM), the charge coupled device (CCD), the Digital to Analog Converter (DAC) and the associated electronics. Traditionally, the model of the FTS is considered as a second order model, a series of process such as the input and output data, the model class and the equivalent standards of the least square method is presented to obtain the model. In order to evaluate the performance of the least square identification method, the model is compared with the one obtained by the traditional frequency response method. The residual sum of squares between these two model outputs and the actual output are 8.20 and 89.52, respectively; while the correlation coefficients are 0.98 and 0.95, respectively. The results indicate that the model of the FTS obtained by the least squares identification method is more accurate than the one obtained by the frequency response method.