The performance of laser beams in tracking Lissajous scan trajectories is severely limited by beam jitter. To enhance the performance of fast steering mirror (FSM) control in tracking Lissajous scan trajectories, this paper proposed a fractional order active disturbance rejection controller (FOADRC) and verified its effectiveness in improving system scanning tracking accuracy. A dynamic mathematical model of a fast steering mirror was studied, and the design of parameters for the control mode of the closed-loop system was determined. A reduced-order linear active disturbance rejection controller suitable for FSM systems was designed, and the corresponding fractional-order proportional differentiation (FOPD) controller was determined according to the mathematical model. The use of the designed controller enabled high-performance tracking of high-frequency Lissajous scanning curves (X-axis 500 Hz, Y-axis 350 Hz) and met the need for high-frequency repetitive scanning. The controller has the characteristics of simple implementation and low computational complexity and is suitable for closed-loop control applications in engineering.