The root mean square gradient (GRMS) is a key parameter for KH2PO4 crystal of low-frequency wavefront, which affects the focusing performance in the inertial confinement fusion (ICF) system. The large wavelength waviness on the machined surface has significant influence on the GRMS. In this paper, the influence of the large wavelength waviness on the GRMS and the main sources resulting in the large scale ripples are analyzed based on dynamics analysis of the machine tool. The dynamic performance of machine tool is optimized and the reasonable dynamic stiffness region is obtained. Furthermore, the machined and the tested results validate the usefulness of the theoretical analysis.