The invention relates to a time synchronization method based on a troposcatter channel. The time synchronization method based on a troposcatter channel transmits a time comparison signal to the troposcatter channel, and includes the following steps: establishing a scatter link; sending a time comparison signal generated by a master station atomic clock to a pulse gate, obtaining a video signal bymultiplying a pulse signal which is obtained through processing by the pulse gate by a sine wave, and sending out the obtained video signal through a signal transmitter; sending a time comparison signal to the time interval counter from a slave station atomic clock, and starting timing by the time interval counter; after a signal receiver receives the time comparison signal of the master station,sending the time comparison signal to the time interval counter through a low noise amplifier, a band pass filter, an automatic gain control module and a broadband matching filter, and stopping timingand sending the counted value to a time synchronization data processing unit after the time interval counter receives the time comparison signal of the master station; and calculating the clock difference between the master station and the slave station by the time synchronization data processing unit, determining whether the two station is synchronous in time, and if not, then performing calibration. The time synchronization method based on a troposcatter channel has the characteristics of being autonomous, rapid and over-the-horizon.