We report rigorous coupled-wave analysis (RCWA) method to non-destructively characterize the domain structure of periodically poled lithium niobate (PPLN) crystal. The strong light diffraction effect is achieved by applying a proper external voltage. We can observe reversed domain pattern and employ the detected diffraction intensity to optimally fit the result of RCWA based on least square method. Compared with conventional scalar diffraction theory, more accurate domain structure parameters with accuracies of 0.05 μm and 0.005 for the period and duty cycle are obtained respectively. It is proved that accurate, real-time and nondestructive characterization can be realized via this method.