The Baise Basin and the Danjiangkou Reservoir Region (DRR) in South China stand as important areas where handaxe artifacts are concentrated, serving as invaluable resources for understanding the complex details of Acheulean technology in East Asia. These regions have witnessed the discovery of numerous handaxes, which have the potential to contribute to our understanding of the technological and cultural developments in this region. However, previous studies mainly focused on the morphological features of handaxes from particular areas. While such studies have provided valuable insights into the morphological and regional characteristics of these artifacts. Notably, a notable divergence in technological complexity and morphological characteristics across different regions.The absence of cross-regional comparison has limited our understanding of the variations and similarities of handaxes’ morphology across disparate areas. In order to compensate for this shortcoming of prior investigations, this study employs a systematic research methodology. Firstly, a three-dimensional (3D) scanning was applied to collected models of handaxes from both the Baise Basin and the DRR. Subsequently, the AGMT-3D software was utilized to analyze the 3D geometric morphology of these handaxes. Through the generation of heat maps, this software enables an intuitive visualization of the variation extent and characteristics. Heat maps provide a straightforward way to identify areas of high and low variation, allowing researchers to quickly grasp the overall morphological trends. Besides this, a series of advanced statistical methods were employed. Principal Component Analysis (PCA), correlation analysis of principal component scores and the Wilcoxon rank-sum test was applied to reveal the morphological differences among handaxes between the two regions. The results of this study reveal several significant findings. It was found that the morphological variation of handaxes in the Baise Basin is notably higher than that in the DRR, indicating a greater diversity in the shape of handaxes produced in the Baise Basin. Moreover, significant morphological difference exist between the handaxes from the two regions. Specifically, the handaxes in the Baise Basin exhibit lower elongation, thinning index, and tip contraction compared to those in the DRR. Such differences in morphological characteristics may suggest that the handaxes from these two regions might have fulfilled different function, been crafted from different types of raw materials with distinct properties, or been influenced by different cultural traditions and chronological factors. In conclusion, this research offers key evidence for a more profound understanding of the morphological feature of Chinese handaxes and the diversity and variability within Acheulean in East Asian.