SummaryThe direct drive manipulator, which directly links the joint shaft to the motor rotor, is susceptible to external disturbances and model perturbations. When the direct drive manipulator operates with varying payloads, the disturbance observer (DOB) with a constant nominal model struggles to achieve satisfactory performance. To minimize estimation errors caused by disturbance, enhance trajectory tracking accuracy, and improve system robustness, this article proposes a controller parameter self‐tuning strategy with settling time, fused with a nominal model adaptive disturbance observer. Specifically, by optimizing the gain coefficient of the model reference adaptive identification (MRAI), the significant changes in payload at the manipulator's end joint can be quickly and accurately estimated. The inertia introduced by the payload is then employed to continuously update the nominal model of the manipulator, incorporating information about the inertia of the coupling joints. In addition, the controller parameters are updated using a self‐tuning link with settling time, which guarantees that the closed‐loop characteristics of the system remain unaffected by payload changes. Finally, the proposed method was validated using a two‐joint direct drive manipulator. The results demonstrate the robustness of the proposed method in the presence of significant payload changes, and the accuracy of disturbance estimation and the tracking performance of the proposed control strategy is significantly improved.