To improve the on board data handling ability, an on-board electronic system required further optimization. On the basis of present reconfigurable on-board computer design, the paper introduced a concept of multiple core processors. According to the functions of the data handling and limitation of the hardware resource, the tasks implemented by single processor are divided into two parts taken by dual-processors. Compared with on-board computer employed on SY-3, multiple core processors have surmounted the peers in computation speed and calculation accuracy. The result verifies that multiple processors will play an important role in future spacecraft designs.