This paper reports an application of uncertainty visualisation of a regional scale (1 : 50000) 3D geological geometry model to be involved in GIS-based 3D mineral potential assessment of the Xiangxibei lead-zinc mineral concentration area in northwestern Hunan District, China. Three-dimensional (3D) geo-logical modelling is a process of interpretation that combines a set of input measurements in geometry. Today, technology has become a necessary part of GIS-based deep prospecting. However, issues of sparse data and imperfect understanding exist in the process so that there are several uncertainties in 3D geological modelling. And these uncertainties are inevitably transmitted into the post-processing applications, such as model-based mineral resource assessment. Thus, in this paper, first, a big-data-based method was used to estimate the uncertainty of a 3D geological model; second, a group of expectations of geological geometry uncertainty were calculated and integrated into ore-bearing stratoisohypse modelling, which is one of the major favourable parameters of assessment for Lead-Zinc (Pb-Zn) deep prospectivity mapping in northwestern Hunan; and finally, prospecting targets were improved.