<p>Compared with traditional rigid rotating structures, small deformation flexible rotating structures (SDFRS) are lightweight, adaptable, and maneuverable. Thus, the SDFRS is commonly utilized in industrial manufacturing, medical surgery, and space operations. However, the elongated and lightweight characteristic of the SDFRS is prone to induce structural flexibility during the motion. It leads to the problem of the SDFRS’s dynamics modeling and controller designing, which has been a difficult research issue. To address this issue, the dynamics model considering multiple nonlinear factors is built, and the model is simplified to obtain the more precise and solvable dynamics model. Besides, the PI control strategy based on the nonlinear disturbance observer (NDOB) is presented, thereby improving the SDFRS’s rotational motion precision. Firstly, the dynamics model with consideration of multiple nonlinear factors, including external disturbances and longitudinal deformation, is established by the assumed modal method (AMM) and Lagrange’s equations. Then, the dynamic model of the SDFRS is simplified by considering different coupled nonlinear terms. Afterward, the dynamics models are compared and analyzed to obtain a more precise dynamics model. Furthermore, based on the dynamics model, the control strategy combining the NDOB and the traditional PI control method is designed. The NDOB is introduced to observe and compensate for the unknown external disturbances suffered by the SDFRS in the dynamical system. Finally, the numerical simulation analysis and physical prototype control experiments are conducted. The analysis results suggest that the PI control method based on the NDOB is effective in realizing the precise rotational motion while weakening the flexible vibration of the SDFRS.</p>