The Daurian ground squirrel (Spermophilus dauricus) is an important animal model that is frequently used by researchers studying the physiological ecology of hibernation in China. There has been considerable controversy regarding the classification of its subspecies, and there is a lack of relevant comparisons of morphometric data. To clarify this issue, this study aims to systematically compare five external morphological traits and 20 cranial traits of S. dauricus collected from 10 locations within China to assess the phenotypic differentiation of S. dauricus within China. Through morphological cluster analysis (MCA), discriminant function analysis (DFA), and principal component analysis (PCA), the samples from 10 locations (FK, n = 5; JZ, n = 11; DQ, n = 7; KP, n = 6; HEB, n = 4; EE, n = 10; CF, n = 3; ZB, n = 6; CD, n = 8; WL, n = 7) can be divided into three geographical populations: the Northeast population (NE); the Inner Mongolia population (IM); and the Hebei population (HB). There is significant morphological variation in four external traits and 19 cranial traits among populations within the species. Specifically, the NE population presented greater body length, tail length, and cranial dimensions. The IM population has the shortest tail, whereas the HB population has the smallest overall body size—its tail length, however, falls between those of the NE and IM populations. These morphological differences may be related to differences in habitat. This study revealed a significant correlation between environmental factors and the morphological traits of S. dauricus. Redundancy analysis (RDA) further revealed that the mean annual temperature (MAT) and mean annual precipitation (MAP) significantly affected the morphological traits of S. dauricus. This study challenges the current subspecies classification, clarifies the geographical morphological variation pattern of S. dauricus, reveals the influence of the environment on the differentiation of its morphological traits, and provides new morphological evidence for resolving the controversy over its subspecies classification.