The invention discloses a fusion network system for quantum communication and quantum time-frequency transmission and method. A quantum relay unit transmits entangled photon pairs and transmits the entangled photon pairs to two quantum terminal units through transmission units respectively; the quantum terminal unit reflects input photons, and the photons are returned to the quantum relay unit through the transmission unit; the quantum relay unit performs HOM interference measurement on the entangled photon pairs, optical path delay is adjusted, the maximum HOM depression value is obtained through multiple times of measurement, and optical path balance is realized. Later, a signal laser transmits laser pulses to the quantum relay unit through the transmission unit, the quantum terminal unit codes the input laser pulses and transmits the laser pulses to the quantum relay unit through a transmission channel, the quantum relay unit obtains a result, an acquired key is published through aclassical channel, clock synchronization is carried out through the classical channel and by using an optical channel monitor, time-frequency information is encrypted through a key distributed by QKD,and thus, the time-frequency information security problem is solved, and fusion between quantum communication and quantum time-frequency transmission is realized.