[Objectives] Rodents act as crucial hosts in transmitting diseases such as the plague. Having efficient methods to identify rodent species is essential for disease prevention. Species are typically identified based on morphological features such as fur and body structures in the field. However, rodents are highly diverse and have variations within and between species. Examining stable and sturdy skulls can help identify the species considering the unreliability of external appearance. Currently, there is limited research on the morphological distinctions of rat mandibles. We aimed to explore the morphological differences among four rat species in the Yunnan Province, including Rattus tanezumi, R. nitidus, R. norvegicus and R. andamanensis, and provide more efficient and accurate classification criteria for species identification. [Methods] We carried out traditional linear measurement analysis and geometric morphometrics analysis on 40 mandibular specimens (10 for each species). One-way ANOVA analysis was employed to examine the differences in traditional measurements. Principal component analysis, canonical variable analysis, and phylogenetic signal test were used to analyze the differences in the geometric morphology of the mandibles of the four Rattus species. The accuracy of different methods for species identification was tested by Bayes discriminant analysis and function discriminant method. [Results] There were overall significant differences in mandibular length, length of the molar row, mandibular height, and length of the diastema between the four species, with the difference between R. tanezumi and R. andamanensis being the most prominent (Table 1). The results of geometric morphometrics showed that the mandibular morphology of R. tanezumi was similar to that of R. andamanensis, and the mandibular morphology of R. tanezumi was the most different from that of R. nitidus. The morphological differences of the mandible between four species were mainly detected in the coronoid, angular, and condylar processes (Fig. 4 and 6). The species classification accuracy results of Bayes discriminant analysis and discriminant function analysis both showed that the two methods have considerable reliability in species classification accuracy (Table 2 and Fig. 7). [Conclusion] The mandibular morphology can be used as the basis for the identification between the four species. The geometric morphometrics analysis method can help identify species between the four Rattus species. In subsequent studies, this method can be applied to verify additional groups to obtain more extensive information on morphological differences. This will serve as a reference for species identification, further promoting the control and prevention of rodent-borne diseases.