Abstract: The accuracy of delay calibration of inter-satellite link subsystem directly affects dual ranging and high-precision time synchronization of system in-orbit,the common reference state is usually adopted at ground calibration,which requires the support of multichannel output of high stability 10 MHz rubidium referecne, but the calibration state is not completely consistent with the in-orbit application state of system.Aiming at the limitation of common reference, different reference state of delay calibration method is proposed and a detailed error analysis is carried out,it shows the error affected by the reference drift characteristic of the two satellite reference sources, the timeliness of satellite telemetry and the consistency of the state on two satellite 1 PPS. The delay calibration error is about 1.901 ns by different reference state, which can meet the requirements of system.In engineering practice,the different refferenc state of delay calibration has certain reference and application value.