Laser time transfer is of great significance in timing and global time synchronization. However, the temperature drift may occur and affect the delay of the electronics system, optic generation and detection system. This paper proposes a post-processing method for the compensation of temperature-induced system delay, which does not require any changes to the hardware setup. The temperature drift and time stability of the whole system are compared with and without compensation. The results show that the propagation delay drift as high as 240 ps caused by temperature changes is compensated. The temperature drift coefficient was diminished down to ~0.05 ps/°C from ~20.0 ps/°C. The system precision was promoted to ~2 ps from ~11 ps over a time period of 80,000 s. This method performs significant compensation of single-photon laser time transfer system propagation drift and will help to establish an ultra-stable laser time transfer link in space applications.