High-precision comparison of time-frequency is an important technology to achieve high-precision time-space consistency and time-frequency stability of the whole society information system, and provides a unified time guarantee for key areas of national economic development. Owing to its high detection efficiency, low noise, low timing jitter, and easy integration, silicon single photon detector is the key core chip in the high-precision satellite-to-ground time comparison system. The interrelationship between photon detection efficiency, dark count rate and timing jitter of the silicon single photon detector was analyzed in this paper. Based on the in-depth review of the research of the silicon single photon detector, the relationship between photon detection efficiency and timing jitter was effectively overcome. A silicon single photon detector with a photosensitive diameter of 200 μm, photon detection efficiency of 50% at room temperature, and the timing jitter of 46 ps was developed. Its application in the satellite-to-ground time comparison was briefly introduced finally.