SUMMARY Determining a detailed 3-D velocity model with high resolution for the sedimentary layer in the Sichuan Basin is potentially beneficial both to the industrial oil/gas exploration and earthquake hazards’ mitigation. In this study, we apply the ambient noise tomography method to construct a 3-D S-wave velocity model. This model focuses on the sedimentary layer of the Sichuan Basin, with a 0.3° × 0.3° grid precision. Dispersion curves of both group and phase velocities of Rayleigh wave at 4 to 40 s periods are utilized, which are extracted from 87 broad-band stations in the Sichuan Basin and the surrounding areas. The 3-D model reveals a thick sedimentary layer of the Sichuan Basin with S-wave velocity ranging from ∼2.0 to 3.4 km s−1. The sediment thickness in the margins of the Sichuan Basin is generally greater than the typical values of 6–10 km in the central areas due to surrounding orogenic activities, with a maximum depth of ∼13 km in the northwestern margin. Moreover, a prominent low S-wave velocity anomaly in the margins may be caused by the sediment accumulations from large-scale landslides and pronounced denudation of the surrounding orogenic belts. Major geologic units in the sedimentary layer are delineated in this study. The S-wave velocity values within each geologic unit and their bottom interfaces are obtained. Based on our model, we calculate synthetic ground motions for the 2013 Lushan earthquake and obtain the distribution of the peak ground acceleration from the earthquake epicentre to the western Sichuan Basin. The result clearly illustrates the basin amplification effect on the seismic waves.