The soil-rock mixture sedimentary stratum is a compound with complex and loose topography, of which the structure is difficult to detect by the ordinary geophysical method. There is a need for a convenient, efficient and effective geophysical method to detect site effects in this area. This paper is an application of the S wave velocity profile inversion for the soil-rock mixture sedimentary stratum, using HVSR (Horizontal to Vertical Spectral Ratio) analysis of ambient noise by some three-component observations in the Chinese Loess Plateau. We carried out the measurement using three nested circular arrays and data recording systems with a spectrum expansion circuit. Inversion of the HVSR curves was performed by a three-layer model. Results of geological observation reveal that the upper part of the sedimentary stratum is Quaternary strata containing a large amount of humus and loess, the middle layer part is the stratum of the loose gravel and the under part is completely weathered granite with homogeneous lithology and fewer rocks. Interpretation results are consistent with previous drilling data, providing a valid geophysical basis for evaluating the stability of the soil erosion and designing a reasonable water and soil erosion control scheme.