Abstract: To achieve ground motion prediction, it is necessary to build a 3-D velocity structure model of sedimentary basin. Taking the Yuxi basin as an example, we provide a modeling procedure, including data preprocessing, model building, model updating and model testing. Based on the different credibility of various data, we propose a function that can eliminate the velocity deviation among various data. In this paper, an improved model updating method is proposed in order to avoid the dependence on the seismic waveform data and the simulation of the microtremors spectral ratio of horizontal to vertical component (H/V spectra). We apply the theory that the H/V spectral shape of the fundamental-mode Rayleigh, including its peak and trough periods, is similar to that of the microtremors to update the 3-D velocity structure model. When the depth of each sedimentary layer in the velocity structure under a single microtremors measuring point is increased by about 15 m, the H/V spectral peak and trough periods of the fundamental-mode Rayleigh wave will both increase about 0.1 s, moreover, the two periods are controlled by deep or shallow velocity structures of the sedimentary layers in basin respectively. Because of the convenient acquisition of the microtremors data, the model updating method has extensive applicability. The 3-D velocity structure model of the Yuxi basin modified by the model updating method has been confirmed a high accuracy after inspection.