The sorting and restoring of source packets of satellite payload data is an important part of a ground data processing flow, and its correctness and completeness directly affect data-based scientific research. This study analyzes the abnormal data and challenges to source packet sorting in ground data processing brought by the satellite data organizations and satellite-ground data transmission mechanisms under the current international standard—the consultative committee for space data systems (CCSDS) standard. On this basis, it proposes a “multiple indexes and timestamp correction” packet sorting method, which not only solves the difficulties in duplicate data elimination and data registration of ground source packets caused by the frequent acquisition of data about space science satellites but also gives correct results in face of key index abnormalities such as abnormalities in the frame serial number, packet serial number, and timestamp. This method has effectively promoted the accuracy of source packet sorting and data processing efficiency of China’s space science missions.