The deep internal structure of the crust can be determined using appropriate seismic and electromagnetic methods. The natural source magnetotelluric (MT) method is the most suitable electromagnetic technique for probing into the deep crust. A long period magnetotelluric data set obtained in the Southern Chilean Andes is investigated in this paper. Dimensionality analysis shows that the data may be regarded as with a strike 2D direction aligned to the N-S direction. Results of a joint inversion of different MT data types indicate relatively high conductive structures in the middle to deep crust beneath the volcanic arc.