To reveal the morphological diversity of the Apis cerana cerana population in the Mount Fanjing National Nature Reserve and its relationship with geographical distribution, this study aims to provide a scientific basis for the conservation of germplasm resources and the screening of superior honeybee strains through morphological indicator analysis. The research focused on A. cerana cerana within the Mount Fanjing National Nature Reserve, investigating 21 different sample populations and conducting a comparative analysis of 39 morphological indicators.The results showed that there were certain differences among the A. cerana cerana populations in the Mount Fanjing Reserve, with significant variations in proboscis length, right forewing length, cubital index, the length of the third tergite, and the width of the black hair band on the fourth tergite. The reserve's honeybees exhibited the richest color patterns in the clypeus and scutellar Sc region, while the upper lip color pattern was relatively uniform (only grade 5). The scutellar Sc region was predominantly grades 7-8 (85.78%), with a yellowish hue, and the KB region was mainly grades 4-6 (61.75%), showing a moderately yellowish hue. The abdominal tergite color pattern was predominantly 8-7-7, with the second tergite displaying a yellowish hue in 91.57% of the samples. Principal component analysis extracted two principal components, cumulatively explaining 51.41% of the variation. Factor 1 was closely associated with morphological indicators related to foraging ability and wax secretion, while Factor 2 was related to body size and color intensity. Cluster analysis divided the 21 sample populations into two major categories: the first category was mainly distributed in the northeastern and northern parts of Mount Fanjing, showing a clear geographical distribution pattern, while the remaining regions clustered into another category. The honeybees from the Guizhou University experimental field formed a separate group. The honeybees from Yinjiang (samples 19 and 18) exhibited strong production capabilities, while those from Songtao and Jiangkou (samples 15, 9, 8, and 1) had larger body sizes and strong flight abilities, making them potential candidates for superior germplasm resource conservation.