High contour accuracy is vital to the multi-axis motion system. Improvement in the contour accuracy of the parallel kinematic machine (PKM) has being a challenging issue in the process of its practical application. In analogy to the intelligent structure of the organisms, this paper proposes a smart structure based compensation (SSBC) method to improve the PKM's contour accuracy. Instead of adopting the advanced control strategies or improving the performances of machine's hardware, this method deals with the contouring issue through innovative mechanical design. The smart structures, which have the ability of perception and control, are introduced into the PKM's components to actively suppress their deformations and vibrations. Meanwhile, the accurate micro motions provided by the smart structure components can be used to compensate for the PKM's contour error caused by the uncoordinated control of the driving system just by using a simple control strategy. The implementation procedure of the SSBC method is first discussed in detail. A 2-DOF PKM is taken as the application object and the smart structures are introduced into its kinematic chains to control their axial deformations and internal forces. Then this PKM's kinematic error is reduced in advance to guarantee the result of the contour accuracy improvement. Finally, several experimental tests are performed to verify the effectiveness the proposed SSBC method in improving the PKM's contour accuracy. Except for the PKM, the SSBC method also provides a novel and effective way for the advanced multi-axis machines to improve their contour accuracies.