Research conclusions:In the research on the alignment of the Zhongtiaoshan Tunnel，the natural source audio frequency magnetotelluric was used for the geophysical exploration to find out the stratum condition and unfavorable geological structures in the survey area，achieving the expected survey target．During the exploration for the Zhongtiaoshan Tunnel，the 11 Class － I geophysical abnormalities，8 Class － II geophysical abnormalities and faults of F2、F3、F4 were deduced，and to them the more attention would be paid during construction．The magnetotelluric method has the featurs of simple out － door application，low cost and deep depth detecting due to using the natural MT signal as the field source．As the AMT uses higher band frequencies，it has higher resolution in the shallow areas．It is available for the engineering investigation，and the desirable results of the explorartion for the Zhongtiaoshan Tunnel was achieved．