The concealed (>80 m) Baiyinnuoer Pb-Zn deposit in Inner Mongolia is a typical skarn deposit in North China and has been studied to improve geochemical exploration within the area. Two vertical soil profiles were studied in order to evaluate the vertical geochemical distribution patterns within the residual soil associated with this deposit. Soil Profile #6 is located above the Pb-Zn orebody whereas Profile #8 is located away from this deposit. To determine the dynamics of the vertical geochemical distribution patterns, concentrations and species of nine elements in samples of six different size fractions were used. The distribution patterns of all the nine elements along Profile #6 display a similar trend of lower concentrations in both the topsoil and moderately-weathered bedrock layers but higher concentrations in the residual subsoil layer, showing a inverted ‘C-shape’. The normalized concentrations (using Fe) of elements and the normalized enrichment factors also follow the same distribution patterns. A sequential extraction study of the soil showed that ore-forming and pathfinder elements were dominantly related to humic acid, Fe-Mn oxides and residual fractions. Based on the results, the recommended soil sampling depth for detecting surficial geochemical anomalies in this and similar semi-arid and thickly covered area is 2–3 m. Furthermore, Hg, Sb, As, Cu, Pb, Zn, Mn and Bi appear to be important indicators for geochemical exploration of Pb-Zn deposits. The research approach and results of this study are useful for evaluating mineral resources in similar covered areas through surface geochemical soil surveys as well as for providing insights to the dynamics of vertical geochemical patterns in soil from concealed Pb-Zn deposits.