In order to clarify the population characteristics of Apis cerana cerana in Yuexi County and Jingxian County of Anhui Province, and accurately reveal its population differentiation in Anhui Province, this study carried out relevant experiments. Twenty honeybee colonies were sampled from each region (15 adult worker bees per colony). Thirty-eight morphological traits were measured using a stereomicroscope. Data were analyzed using SPSS23.0, including variance, cluster, discriminant, factor, and correlation analyses. Significant morphological differentiation was observed between the two populations (P<0.05). Twelve key morphological indices including hind-leg, tergum, and forewing width，exhibited positive correlations with latitude, altitude, and mean annual rainfall. Conversely, pigmentation indices showed a negative correlation with altitude. Principal sources of morphological variation were identified as hind-leg length (accounting for 11.69% of total variance), scutellum pigmentation (6.21%), width of the pubescent band on tergum (5.38%), and forewing length and width (4.82%). Cluster analysis revealed that the samples from the two counties independently grouped into two distinct clusters. Apis cerana cerana exhibits significant morphological diversity between Yuexi and Jingxian. The high-altitude environment of Yuexi appears to select for larger body size and darker pigmentation. Significant geographical differentiation exists between the populations, providing a foundation for classifying geographical populations of Apis cerana cerana within Anhui Province.