The invention discloses an S transform domain Q value estimation and compensation method based on the variational principle. A nonstationary seismic record convolution model is introduced to S transform, firstly, S transform of a seismic record is carried out, compared with the time domain and frequency domain method, nonstationary characteristics of the seismic record can be more intelligibly represented in the time frequency domain, Q value estimation is carried out based on the variational principle, windowing processing on the seismic record is not needed, influence of a window function on the Q value estimation result can be reduced, moreover, as integral processing on the whole seismic record is carried out, the absorption and scattering coupling effect during reflection seismic data processing can be avoided, stronger anti-noise performance is realized, and inversion parameter precision is higher.