This article proposes an online identification method for a electro-optical tracking system based on the Zynq platform, addressing the cumbersome and inefficient nature of traditional identification. By designing data acquisition and driver programs for A/D and D/A modules, real-time collection and control are achieved, and running the VxWorks operating system on Zynq platform. The use of FFT technology enables the online measurement of frequency characteristics, and a hybrid improved quantum-behaved particle swarm optimization algorithm with natural selection parameters is employed for system identification. Experimental results demonstrate that this method possesses high-precision frequency characteristic measurement and accurate system identification capabilities, providing effective means for real-time control and optimization of electrooptical tracking systems.