The invention discloses a time frequency analysis method of magnetotelluric impedance estimation. By adopting empirical mode decomposition technology of Hilbert-Huang transform, a magnetotelluric signal is decomposed to acquire mode functions of various orders for the Hilbert transform, and the time frequency spectrums of the four components of the magnetotelluric signal are acquired, and acquired instant amplitudes are used to replace Fourier spectrum of a conventional Fourier method, and then the instant amplitudes are introduced in a minimal quadratic equation to solve impedance tensors of time frequency points, and then the impedance tensor elements of the various time frequency points are calculated, and in addition, the time frequency power spectrogram of the magnetotelluric signal is converted into a time frequency impedance spectrogram. In the time frequency impedance magnetotelluric, the response function values of the various time frequency points having same instant frequencies are accumulated together, and then the acquired sum is divided by the number of the time frequency point, and the mean value thereof is a response function estimated value of a frequency value. The time frequency analysis method of the magnetotelluric impedance estimation is advantageous in that realizing of robust estimation is facilitated, and the impedance elements acquired by adopting the method conform to reality of a stratum structure, and a stronger noise inhibition capability is provided, and an estimation result is more robust.