The invention provides a time synchronization method and system in quantum secret communication. The time synchronization method comprises the following steps: S1, emitting signal light and synchronous light; s2, coupling the signal light and the synchronous light and then transmitting the coupled light through the same few-mode optical fiber channel; s3, receiving the coupled signal light and synchronous light and splitting the signal light and synchronous light; s4, detecting the signal light and the synchronous light, determining link transmission delay between the signal light pulse and the synchronous light pulse, and performing synchronous correction on the signal light; s5, performing frame numbering on the synchronous light, and labeling each signal light pulse according to the time interval between each signal light pulse and the synchronous light pulse of the frame to which the signal light pulse belongs; s6, identifying the frame number of the synchronous light, and measuring the time interval between the signal light pulse and the synchronous light pulse of the frame to which the signal light pulse belongs; judging the label of the received signal light pulse accordingto the time interval; and enabling the received signal light pulse labels to be in one-to-one correspondence with the sent signal light pulse labels.