With the boost in the number of spacecraft launches in the current decades, the space debris problem is daily becoming significantly crucial. For sustainable space utilization, the continuous removal of space debris is the most severe problem for humanity. To maximize the reliability of the debris capture mission in orbit, accurate motion estimation of the target is essential. Space debris has lost its attitude and orbit control capabilities, and its shape is unknown due to the break. This paper proposes the Structure from Motion-based algorithm to perform unknown shaped space debris motion estimation with limited resources, where only 2D images are required as input. The method then outputs the reconstructed shape of the unknown object and the relative pose trajectory between the target and the camera simultaneously, which are exploited to estimate the target's motion. The method is quantitatively validated with the realistic image dataset generated by the microgravity experiment in a 2D air-floating testbed and 3D kinematic simulation.