The invention provides a method for calculating the three-dimensional magnetotelluric sounding main impedance, and belongs to the field of electromagnetic exploration of geological exploration and underground mineral resource exploration such as petroleum, natural gas, and shale gas etc. The method includes: (1) acquiring time domain recording data obtained via field acquisition, wherein the data comprising an electric field and a magnetic field in the mutual vertical direction, namely ex (t), ey (t), hx (t), and hy (t), and t referring to time; (2) performing conversion of the time domain recording data in step (1) from time domain to frequency domain; (3) calculating the tensor impedance original value and performing editing processing of the original value; (4) calculating a correct coordinate rotation angle theta0; (5) calculating the main impedances a and b in the three-dimensional construction condition; (6) calculating three-dimensional scattering tensor factors e, lambda1, and lambda2; and (7) giving a calculating result of the coordinate rotation angle theta0, a three-dimensional scattering tensor factor C, and the main impedance Z0.