Using single point diamond turning method to process KDP crystals, the micro-waviness, which has a significant impact on the laser induced damage threshold, will be left on the machined surface. The effect of micro-waviness on near-field light intensity distribution was analyzed by Finite Difference Time Domain (FDTD) method. Results indicate that: the micro-waviness will distort the incident wave and lead to periodic distribution of strength and weakness of light intensity along x- and z-axis inside the KDP crystal. When the micro-waviness period is below 0.7 μm, it has a low influence on the modulation of light intensity inside the crystal. Meanwhile, the light intensity modulates around the micro-waviness in the form of evanescent wave. Relative light intensity reaches the maximum in the period of 1.064 μm, and remains unchanged above the period of 3 μm. In the common range of the micro-waviness amplitude, the relative light intensity increases linearly as the micro-waviness amplitude increases, with different slope in different micro-waviness period.