Abstract: According to design characteristics and configuration of Mars orbiter, the whole link time calibration of mars orbiter was studied and validated, the time transmission path of Mars orbiter was analyzed, and a whole link time calibration method suitable for Mars exploration missions was given. Time calibration of hardware equipment, software design and system configuration was introduced. The actual application results show that the calibration method of the whole link time of Mars orbiter was reasonable, the launch day timing was accurate, and the ground test data were verified by the actual operation in orbit. This paper provides important reference for the design of time calibration system and calibration method for subsequent Mars exploration and related deep space missions.