Skeletons serve as the body’s fundamental structure and perform multiple vital functions, and thus even subtle modifications can lead to functional changes. However, studies on sexual shape dimorphism in the appendicular skeletons of anurans remain scarce, especially for fossorial species. Herein, we investigated the sexual differences in the external morphology and internal skeletal shape of girdles and limbs of fossorial Kaloula rugifera during the breeding season. The results reveal the following: (1) Males exhibit significantly longer forelimbs and hindlimbs, suggesting advantages in male—male competition and amplexus. (2) Males possess more curved and dilated coracoids and broader pubis-ischium regions, which may enhance forelimb contraction efficiency and hindlimb locomotor performance. (3) Males feature a more developed crista ventralis, likely enhancing forelimb flexion for tightly grasping females during mating. In contrast, females display a torsioned femur and robust hindlimb morphology, suggesting adaptations for digging and load-bearing. These findings provide insights into how anurans optimize reproductive fitness and ecological adaptations through morphological specialization. To our knowledge, this study presents the first examination of sexual shape dimorphism in anuran appendicular skeletons utilizing three-dimensional geometric morphometrics.