Underground silt is commonly found in southern cities with well-developed water systems in China. It poses safety and quality risks to urban infrastructure construction due to its complex composition and poor engineering properties. It is of great importance to identify the spatial distribution characteristics of underground silt before engineering construction. This study takes the investigation of the underground silt of Ningbo Rail Transit Line 7 as an example, employing the high-density resistivity method and microtremor survey for comprehensive detection of the spatial distribution characteristics of underground silt. The comprehensive geophysical prospecting results are used to guide the geological drilling implementation, and their reliability is further verified based on the geological drilling results. Traditional microtremor data processing methods struggle to achieve high lateral resolution for detecting local subsurface heterogeneities. This study employs Multiscale Window Analysis of Surface Waves (MWASW), overcoming the limitations of traditional methods in terms of lateral resolution and enabling accurate delineation of the undulating morphology of underground silt basal boundaries. The high-density resistivity method has good resolution in both horizontal and vertical directions, but the identification of anomalies involves uncertainties or nonuniqueness merely based on resistivity inversion. The two geophysical prospecting methods are mutually complementary and verified quite well, effectively identifying the spatial distribution characteristics of the underground silt, with less than 8% depth error compared to drilling-revealed basal boundaries. It is concluded that the integrated geophysical prospecting technology combining microtremor survey and high-density resistivity method, supplemented with limited geological drillings, achieves both detection accuracy and operational efficiency in underground silt exploration. This successful application can provide a reference for geophysical prospecting in similar projects.