Prostatic hyperplasia and tumor are common diseases, and the minimally invasive surgery inserting the instruments through the urethra into the prostate is commonly conducted. Taking the robotic manipulator for such surgery into consideration, this paper analyses the workspace of the end effector, and proposes the distribution error of the fixed point and the tracking error of manipulator end effector on the cone bottom surface of the workspace as the basis for control implementation of the manipulator. The D-H coordinate system of the manipulator is established and the trajectory planning of the end effector in the Cartesian space is carried out. The digital model was established, and dynamics simulation was performed in Solidworks and Matlab/Simulink environment to guide the manipulator design. Trajectory mapping and synchronization control between virtual model and the actual manipulator are realized based on digital twin technique. The virtual manipulator can reflect the real-time state of the manipulator with data interaction by comparing the dynamics simulation results with the motor current values obtained by experiment. Experiment was carried out with PD feedback control and Newton–Euler dynamics based feedforward control to get the trajectory tracking characteristic of each motor, errors of the fixed point and tracking performance of the end effector of the manipulator. The results show that compared with PD feedback control, feed forward control implementation can achieve a reduction of 30.0% in the average error of the fixed point of the manipulator and a reduction of 33.3% in the maximum error.