In recent years, with the implementation of three-dimensional deep geological mapping and shale gas bearing basin prospective evaluation, magnetotelluric method, as one of geophysical methods, has become more and more important. There are a finite number of challenging problems in magnetotelluric data processing and interpretation such as impedance tensor rotation, TE and TM mode identification, static distortion correction, and selection of TE and TM for 2D inversion. Based on magnetotelluric module in WinGlink software, the authors adopted five impedance tensor rotation methods and three curve smoothing methods to process the magnetotelluric data gathered in Jarud Banner, Inner Mongolia. Three stations with different qualities in one profile were chosen to process. The results of five rotation methods and three smoothing methods were analyzed and assessed. Polar diagram analysis of three stations showed that the geological models under themselves were three-dimensional. The comparative study is critical for three-dimensional geological models, and is especially much instructive to the processing and interpretation of magnetotelluric data by using WingGlink software.