Flexible articulated manipulators are often used for the task of tracking reference trajectories in space and have attracted much attention. Aiming at the uncertainty of the robot system, based on random matrix and screw theory, this paper constructs a trajectory control model of a flexible joint manipulator. In order to reduce the steady-state tracking error, a random matrix variable structure control method is introduced into the model, and a nonlinear spinor-like random matrix function is designed to improve the traditional random matrix surface. In the simulation process, the dynamic model of the series robot is firstly obtained according to the screw and random matrix equation, and the dynamic characteristics are analyzed. Combined with dynamic surface control technology, a neural network controller is designed to solve the problem of dimensional explosion and ensure that the tracking error converges to a small neighborhood of zero. The experimental results show that by using the observation value to replace the unmeasurable state of the system, combining it with the random matrix network to identify the unknown dynamics of the system, and designing the random matrix network controller, the tracking control of the system can be realized, and the tracking error can be ensured to converge to a small neighborhood of zero. The control system has a better control effect than traditional PID, the peak time is shortened by 45.83%, the adjustment time is shortened by 46.91%, the maximum overshoot is reduced by 51.35%, and the steady-state error after filtering is only 0.049, which is reduced by 47.31%. Effective interference signal and measurement noise are suppressed, and the quantitative observation performance of the flexible joint manipulator system is improved.