The three-axis parallel motion platform (TAPMP) with a common stator has low motion inertia, enabling highly precise and high-speed motion over a large range of strokes. The primary challenge faced by the TAPMP lies in the mutual pulling exerted between the common stator motors during motion. The driving forces generated by the motors are closely associated with their synchronization motion, a connection often overlooked in the design of existing controllers. To address this issue, this paper presents a novel synchronization controller with dynamics compensation (SC–DC) to achieve motion synchronization between the three motors, ultimately enhancing the platform’s tracking accuracy in task space. In this SC–DC method, the synchronization error of the common stator motors is introduced to represent the synchronized motion relationship between adjacent motors, and a dynamic feedforward control is adopted to compensate for the motor’s driving force. The stability of the proposed controller is analyzed using Lyapunov theory, demonstrating the convergence of both the tracking error and synchronization error. Trajectory tracking simulations and experimental studies are conducted on the TAPMP. The results show that, compared to the augmented proportional-derivative controller with dynamic compensation, the proposed controller significantly reduces both the MAE of the tracking error and synchronization error on the q1 motor by 71.88% and 73.02%, respectively, demonstrating its performance advantages in trajectory tracking and synchronization.