The precision remediation and redevelopment of contaminated sites are crucial issues for improving the human settlement and constructing a beautiful China. Three-dimensional delineation of soil pollutants at contaminated sites is a prerequisite for precision remediation and redevelopment. However, a contaminated site is a three-dimensional complex system coupling multiple spatial elements above-and under-ground. The complexity incurs high uncertainties about the three-dimensional delineation of soil pollutants based on sparse borehole and spatial statistics and inference models. This paper first systematically reviewed the objectives of fine three-dimensional delineation of soil pollutants, the sampling strategies for soil boring, the commonly used models for delineating soil pollutants, and the relevant cases of applying these models at contaminated sites. We then summarized the effects of borehole data and three-dimensional models on soil pollutants' delineation results from biased characteristics and nonstationary conditions. The present research status and related issues on correcting the biased characteristics and nonstationary conditions were analyzed. Finally, based on the problems and challenges, we suggested the three-dimensional delineation of soil pollutants in the underground "black box" for future research from the following six priority areas: multi-scenarios, nonstationary, non-linearity, multi-source data fusion, multiple model coupling, and the delineation of co-contaminated sites.