Attenuation in the shallow weathering zone is relatively strong, causing severe energy loss during wave propagation. It is difficult to estimate accurate values in the shallow weathering zone, and the influence of shallow weathering zone is seldom considered into attenuation estimation and compensation in the deep part. We achieved value estimation where there exist microlog data in the shallow weathering zone using the generalized S transform (GST); then, we establish an empirical formula using the velocity and value estimated with microlog data; finally, the value in the 3D shallow weathering zone can be obtained using the established formula and the velocity information. During the first procedure, the GST is used to provide reasonable time-frequency resolution, and linear regression is used in the obtained logarithmic spectral ratio to get the estimated value. An empirical formula is established using the estimated value and the velocity where there exists microlog data in the second procedure. In the third step, estimation in the whole shallow weathering zone can be obtained using the established formula and the velocity information, which can overcome the inaccuracy of spatial interpolation with the estimated factors where there exist different twin-well microlog data. Attenuation compensation to seismic data obtained from the deep part is carried out to prove the effectiveness of the estimated in the shallow weathering zone. After compensation, the resolution of seismic data is effectively increased, which demonstrates the validity of the estimated values in the shallow weathering zone. Synthetic data and field data examples demonstrate the validity of our method.