The invention discloses a loading task running control method aiming at the radar satellite on-orbit application. The method is characterized in that on the basis of a conventional remote sensing satellite loading task executing mode, the constraint condition of a ground running and controlling system is quantified, and the formats of an application task schedule and an application task data block are appointed, so that the running and controlling of the ground to a satellite is facilitated; meanwhile, the contents of detailed instruction groups, time constraint and compiling requirement in the instruction groups as well as task conflict interpretation and conflict handling requirements are transferred to a satellite on-orbit data management system from the ground running and controlling system; furthermore, a task legality autonomic interpretation control mechanism, a task block deleting and task revising mechanism and a earthward system telemetering feedback mechanism are added on the satellite, so that the loading task autonomic arrangement and control of the radar satellite on-orbit application is realized, and the conventional control convenience and emergency control ability of the satellite on-orbit running are improved; in addition, through providing an on-orbit software modification function, the reliability and safety of the satellite on-orbit application are greatly improved.