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Because the semiconductor infrared and photomultiplier tube single photon detectors are affected by noise data, the photon counting statistical results are inaccurate, resulting in poor control effect after the application of the tracking system. Using avalanche photodiode to detect incident light and avalanche phenomenon, the high-speed single photon detector is improved. Through the feedback control part, the quenching is realized, the avalanche is terminated, and the voltage is restored to the bias voltage. Using the improved detector to design the single photon detection signal detection circuit, the required reference level is obtained, and the hardware structure of the composite tracking control system is designed. The counting control flow of signal transmission is designed, and the tracking degree of high-speed single photon detector and single factor is determined by combining the discrimination formula. Adjust the trigger signal emitted by the single photon detector, determine the photon number of the combined tracking pulse according to the obtained signal, adjust the tracking scheme based on this, and complete the system software structure design. The experimental results show that the improved high-speed single photon detector achieves 220 counts at 38.5ns, which is consistent with the actual results and has a good tracking control effect.