In order to make up for the shortcomings of traditional recognition and research methods, such as the field outcrop, logging and earthquake and so on, 3D Magnetotelluric(MT) is used for the research of sedimentary facies. Through to 3D MT data pretreatment, such as de noising, editing and smothing, static shift correction and so on, and 3D inversion treatment, it is more accurate to reflect the resistivity of sediments from study area. Based on the observation of field outcrop and well logging interpretation, the resistivity value range of different rocks of the Kuqa Fomation is determined, which is calibrated by cores or cuttings. And then stratigraphic framework is established by corrected 3D MT profile congruent to seismic profile. Finally sedimentary facies in the period of Kuqa Formation are recognized and researched finely in stratigraphic framework. The method has obtained favorable application effects in the recognition and research of spatial distribution characteristic of sedimentary facies in the period of Kuqa Formation in the Kuqa Depression. What is more, the problems of sedimentary facies belt changed among wells and unconspicuous characteristics of seismic facies are solved, which is significant to research base oil geological such as distribution of sedimentary facies, sedimentary evolution and so on.