In order to solve the high-precision motion control problem of the n-degree-of-freedom (n-DOF) manipulator driven by large amount of real-time data, a motion control algorithm based on self-organizing interval type-2 fuzzy neural network error compensation (SOT2-FNNEC) is proposed. The proposed control framework can effectively suppress various types of interference such as base jitter, signal interference, time delay, etc., during the movement of the manipulator. The fuzzy neural network structure and self-organization method are used to realize the online self-organization of fuzzy rules based on control data. The stability of the closed-loop control systems are proved by Lyapunov stability theory. Simulations show that the algorithm is superior to a self-organizing fuzzy error compensation network and conventional sliding mode variable structure control methods in control performance.