The invention relates to an organization management method for a three-dimensional model of a complex spacecraft, and belongs to the field of three-dimensional model management. In the method, the three-dimensional model of the complex spacecraft is stored in a PDM (Pulse Duration Modulation) management platform based on concurrent engineering, and an organization structure and a working mechanism in which a mechanical general designer is taken as a main body, a spacecraft production department and each subsystem designer participate, and an information center supplies technical support are established. Corresponding authorities are set specific to the role and task of each member in a spacecraft design team, an effective planning and management are performed on the three-dimensional model, so that multi-person coordinated design based on the three-dimensional model of the spacecraft is realized.