Abstract: In view of remote sensing satellite’s characteristics of covering a large area, high mission frequency, long duration and heavy data updates burden, a satellite multi-payloads autonomous census mission method was proposed. First, the satellite observation mission area was analyzed to identify the priority area and determine the conditional statements and mission sequence according to satellite on-board resource constraints based on payload selection. Then, an autonomous census mission mode was deployed on the satellite to control target observation area selection, judgment of conditional statements and mission sequence selection. At the same time, based on the time interval between two mission cycles, an appropriate mission instruction sequence was selected and autonomous census observations were repeated to form an autonomous operation of the satellite’s long-cycle census work. The ground verification system set up 5 simulation conditions including 2 different types of orbital parameters to test the stability and accuracy of the autonomous census mission mode execution on the satellite under various load configurations. The results show that the designed autonomous census mission mode can accurately judge the entry and exit of the observation area according to the expected timing during satellite operation, and the calculation error of the sub satellite point and the sun angle is below 0.5%.