The new electromagnetic catapult microgravity device employs linear motors to drive the experimental module in vertical motion, simulating a microgravity environment. In comparison to traditional drop tower methods, utilizing a catapult for parabolic motion significantly extends the duration microgravity time. However, the linear motor's drive introduces new challenges in ensuring a high level of microgravity quality. To meet the experimental requirements of microgravity science, this paper conducts a model analysis of the segmented dragging system of the electromagnetic catapult drop tower. It proposes a segmented control scheme and designs a displacement-tracking control algorithm for addressing motor coordination issues affecting microgravity levels and the coordination between inner capsule and outer capsule. This ultimately achieves prevention of disturbance from outer capsule to the inner capsule. The practical system has been constructed and put into operation, employing the motor control method outlined in the paper, enabling microgravity time around 4 seconds. This research provides crucial support for the development of microgravity experimental devices.