Tongling area in Anhui Province is one of the most famous ore districts in China. It is an important part of the Middle lower Yangtze River metallogenic belt. To probe the deep crust structure beneath the Tongling ore district, six magnetotelluric (MT) sounding profiles have been deployed in the SinoProbe 03 Project. The analysis of the data dimensionality shows the obvious 2D/3D characteristics for the deep structure of the region. Therefore a 3D inversion is demanded. After sites data select and frequencies decimation, the WSINV3DMT code is used with a reasonable parameter design to obtain the 3D conductivity structure. The model is proved to be a acceptable one by a comparison between the observed data and the model response. The results show the framework of the 2D profiles extracted from the 3D model is consistent with the 2D inversion model except several detailed differences. The electrical characteristics and structure framework of the 3D model is discussed by slices of the model with different depth and different orientation. The local electric difference of the shallow is grater than the deep; the electrical distribution shows a certain degree of segmentation feature in the plane and layered characteristic in the vertical; the distribution of the high resistivity bodies show the range of of the intrusive rock and the deep low resistivity region shows the area of undisturbed lower crust.