The smoothing effect of data interpolation could cause useful information loss in geochemical mapping, and the uncertainty assessment of geochemical anomaly could help to extract reasonable anomalies. In this paper, multiple-point geostatistical simulation and local singularity analysis (LSA) are proposed to identify regional geochemical anomalies and potential mineral resources areas. Taking Cu geochemical data in the Mila Mountain Region, southern Tibet, as an example, several conclusions were obtained: (1) geochemical mapping based on the direct sampling (DS) algorithm of multiple-point geostatistics can avoid the smoothing effect through geochemical pattern simulation; (2) 200 realizations generated by the direct sampling simulation reflect the uncertainty of an unsampled value, and the geochemical anomaly of each realization can be extracted by local singularity analysis, which shows geochemical anomaly uncertainty; (3) the singularity-quantile (S-Q) analysis method was used to determine the separation thresholds of E-type α, and uncertainty analysis was carried out on the copper anomaly to obtain the anomaly probability map, which should be more reasonable than the interpolation-based geochemical map for geochemical anomaly identification. According to the anomaly probability and favorable geological conditions in the study area, several potential mineral resource targets were preliminarily delineated to provide direction for subsequent mineral exploration.