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In this paper, we improve and verify the inversion algorithm and parallel computing program of the three-dimensional magnetotelluric sounding.The refined program do not require much physical memory or CPU quantity.It realizes running the three-dimensional inversion on the ordinary PC computers.Based on the nonlinear conjugate gradient algorithm and the preconditioning method, we improve the preconditioning method, and thenverify the program with theoretical models.Proved by the inversion results of the measured data in KAYABE area in Japan, we demonstrate the practicality of the algorithm, and discuss the advantages and disadvantages of it.