Objective To achieve the geographical discrimination of Fuping goat milk using microwave digestion combined with inductively coupled plasma mass spectrometry (ICP-MS) and chemometric methods. Methods A total of 70 goat milk samples were collected from 7 regions in Shaanxi Province, including Baoji, Hanzhong, Jingyang County and Qian County (both in Xianyang), Weinan, Xi’an and Yan’an. They were lyophilized to milk powder, and after microwave digestion, the digested solution was analyzed using ICP-MS. Principal component analysis (PCA) and orthogonal partial least squares-discrimination analysis (OPLS-DA) were employed to discriminate goat milk from different origins. Results A total of 42 kinds of elements in the milk powder from 7 different origins were detected. The concentrations of K, Ca, Fe, Zn, Si and Na were relatively high, followed by B, Ti, Mg, Al, Cu and Ba, while other elements were found in lower concentrations, particularly the rare earth elements such as Pr, Nd, Sm, Eu, Gd, Tb, Dy, Er, Tm, Yb, Lu, Ho and Y, which were present in negligible amounts. The 7 origins were divided into two groups based on distance: Group I (Baoji; Hanzhong; Weinan; Yan’an) and Group II (Jingyang County, Qian County of Xianyang; Weinan; Xi’an). OPLS-DA model was applied to both groups, with accuracy rates of 95.12% and 87.80%, respectively. Among them, the accuracy of samples from Fuping County-Weinan City was 100%. In Group I, the content differences of Ba, Mn, Si, Zn, Se, Na and B were the primary factors for origin discrimination. While in Group II, Se, B and Ni elements contributed significantly to the origin discrimination. Geographical distance was the most important factor to distinguish goat milk from different origins. While the data of 6 goat milk samples from Fuping County-Weinan City were imported into both Group I and Group II models for validation, the discrimination accuracy was 100% for both groups. Conclusion The established multi-element analysis combined with chemometrics could achieve rapid and accurate identification of Fuping goat milk from small-scale regions (>50 km).