To meet the high positioning accuracy requirements of precision measurement and machining, a novel sub-micrometer precision XY two-dimensional motion stage system based on system identification and precision drive control method was designed. The system consists of a mechanical structure and a control system. The mechanical part adopts a stacked structure, with the X-axis motion stage located above the Y-axis motion stage, driven by a linear motor and positioned by a grating sensor. To improve the accuracy and stability of the motion stage, a control design method based on frequency domain system identification for large-stroke two-dimensional motion stage systems was proposed. By inputting sinusoidal excitation signals into the servo system and changing the input signal frequency to obtain frequency characteristics and transfer functions, the control parameters such as Kvi-integral gain, Kvp-proportional gain and Kvfr-feedforward gain were optimized. Thus, the high-precision motion of the two-dimensional motion stage was realized. A series of verification experiments were conducted to evaluate the performance of the positioning system. The results show that the two-dimensional motion stage positioning system has a travel range of 240 mm×240 mm, a repeat positioning accuracy better than 1.5 μm, and a drive resolution of up to 40 nm. The developed submicron two-dimensional motion stage system shows good repeatability and stability, can be applied to high-end equipment fields such as precision machining and precision measurement.