High-resolution time synchronization is the crucial technology of quantum key distribution experiment from ground to satellite. A new scheme of time synchronization was presented. In this scheme, a synchronous pulse which has the same wavelength with the quantum signal was adopted and single photo detector was used to detect the synchronous pulse. High-resolution time measurement module was used to measure the instance of synchronous pulse and signal pulse. This scheme overcomes the problem that the the synchronization laser requires much more resources of satellite and the isolation between the synchronization pulse and quantum single pulse. This system was successfully applied to the 16 km quantum key distribution in free space channel. Synchronous resolution of the system is 1.023 ns and bit rate of the raw key for the quantum key distribution is 8.27 kHz.