This paper presents a novel control strategy for transferring large inertia loads using flexible space manipulators in orbit. The proposed strategy employs a Luenberger state observer and damping-stiffness controller to address issues of large tracking error and vibration. A comprehensive joint dynamics model is developed to identify the main sources of disturbance, and a Luenberger state observer is designed to estimate unmeasurable transmission deformation. Transmission stiffness and load inertia perturbations are identified based on the estimated results. By adjusting velocity damping and the gain of the forward channel, perturbations are suppressed to maintain optimal system damping and stiffness. Simulation and physical experiments demonstrate the effectiveness of the algorithm, with simulation experiments showing smoother joint output characteristics and minimal vibration under large load inertia changes, and a 97% reduction in internal deformation. Physical experiments demonstrate improved joint dynamic command tracking performance, with an 88% reduction in position tracking error. The algorithm provides a practical and efficient approach for transferring large inertia scientific payloads in space.