To address the deficiencies of the traditional cross-coupling control structure, an active compensation control structure was proposed in this study to reduce the contour error of an X-Y linear motor precision motion platform. First, a permanent magnet synchronous linear motor was used to analyze the single-axis positioning tracking error, where the tracking error was related to the position reference. Therefore, adjustment to the amount of coupling compensation to the reference instruction was added to the system, which considered the disturbance of the reference command in the actual working condition. The contour error components were compensated to the position and speed loops of each axis servo and verified by a simulation and an experiment. Results show that the average value of the contour error of the X-Y axis motion platform when tracking a large curvature complex track using an active compensation method is 20.68 μm. The single-axis tracking error is 70 μm. Compared with the traditional cross-coupling control structure, the accuracy of the active compensation structure contour error is improved by 15.5%, the single-axis tracking error is reduced, and the reference command disturbance can be suppressed.