The generalized inversion of S-wave amplitude spectra from the free-field strong motion recordings of the China National Strong Motion Observation Network System (NSMONS) are used to evaluate the site effects in the Wenchuan area. In this regard, a total of 602 recordings from 96 aftershocks of the Wenchuan earthquake with magnitudes of M3.7-M6.5 were selected as a dataset. These recordings were obtained from 28 stations at a hypocenter distance ranging from 30 km to 150 km. The inversion results have been verified as reliable by comparing the site response at station 62WUD using the Generalized Inversion Technique (GIT) and the Standard Spectral Ratio method (SSR). For all 28 stations, the site predominant frequency F (p) and the average site amplification in different frequency bands of 1.0-5.0 Hz, 5.0-10.0 Hz and 1.0-10.0 Hz have been calculated based on the inversion results. Compared with the results from the horizontal-to-vertical spectral ratio (HVSR) method, it shows that the HVSR method can reasonably estimate the site predominant frequency but underestimates the site amplification. The linear fitting between the average site amplification for each frequency band and the V (s20) (the average uppermost-20 m shear wave velocity) shows good correlation. A distance measurement called the asperity distance D (Aspt) is proposed to reasonably characterize the source-to-site distance for large earthquakes. Finally, the inversed site response is used to identify the soil nonlinearity in the main shock and aftershocks of Wenchuan earthquake. In ten of the 28 stations analyzed in the main shock, the soil behaved nonlinearly, where the ground motion level is apparently beyond a threshold of PGA > 300 cm/s(2) or PGV > 20 cm/s, and only one station coded 51SFB has evidence of soil nonlinear behavior in the aftershocks.