Abstract: Magnetotelluric is a geophysics exploration method for studying the crust and upper mantle electrical structure, which measures the surface orthogonal electric and magnetic fields based on the electromagnetic induction and natural electromagnetic fields. Thereafter, the audio-frequency magnetotelluric method which collects the high frequency domain of natural field and controlled source audio-freguency magnetotelluric method which collects artificial source are derived. These methods are widely used in deep structure study, mineral resources exploration, oil and gas exploration, and so on. Though the field work achieves 3D level in recent years, 3D data processing and inversion are insufficient and the efficiency and accuracy of interpretation is limited. To solve these problems, we develop the 3D inversion system of magnetotelluric sounding which contains static shift correction, initial model design and 3D inversion. The system effectively solves the static shift of data process and 3D inversion problem. A lot of algorithms in the system are improved which have advantages on calculation accuracy, efficiency and cost savings. And the system has a good application prospect.