Mineral system modeling approach is useful for assessing the likelihood of occurrences of a type of mineral deposit, which are described using two characteristics: spatial scales modeling and relevant geochemical processes. Possible spatial scales include the craton, region, district, and deposit scales. At each scale, geological modeling is an important aid to exhibit favorable features of mineralization at two-dimension (2D) and three-dimension (3D). Commonly, 3D geometry can be used to restructure geological anomaly at deposit and district/camp scales for quantitative mineral resources assessment. However, they are sensitive to input datasets. Thus, in a sense, the reliability of a 3D geological model depends on how much data have been collected at both ground surface and depth. In addition, the components of dataset also constrain what geological modeling method can be used. In this paper, dynamic updatability is considered as one of the metrics to assess 3D geological modeling methods. This paper discusses different 3D geological modeling processes and compares the ease ability to update. A case study was conducted to analyze the ore-bearing formations and structure of a potential Mississippi valley-type (MVT) Pb–Zn deposit in the Huayuan–Malichang District, Hunan Province, China. The contributions of this study include (1) analyzing what kinds of datasets must be collected for geological modeling at deposit and district scales; (2) the use of multiple 3D modeling processes; and (3) comparing metric what updatability between different 3D modeling processes is. Finally, this paper discusses an integration model based on the above demonstration and other studies.