In recent years, the bony labyrinth has gained significant attention among paleoanthropologists due to its ease of preservation and ability to reflect evolutionary signals. Additionally, the morphological features of the bony labyrinth have proven to be indicative of population histories among modern populations. Studies reveal that Late Pleistocene early modern humans (EMHs) in China display mosaic morphological variation. Early modern humans from Longlin, Maludong, Dushandong exhibit archaic traits, whereas other fossil humans, including those from Qihedong and Zhaoguodong, display fully modern features. To investigate this morphological variation and this relationship with extant modern populations, this study examines the three-dimensional morphology of the bony labyrinth in five EMH specimens from China (Liujiang, Ziyang, Longlin, Zhaoguodong, and Qihedong) and compares it to that of modern populations worldwide. Results reveal significant morphological variations in the inner ear labyrinth among modern populations with European and African populations exhibiting similar morphologies but both differing considerably from Asian populations. Asian populations exhibit a cochlea with fewer turns, a more lateral basal position, and a shorter apex, resulting in reduced cochlear thickness. Additionally, the anterior semicircular canal is less torsioned and more anteriorly tilted. These features contrast with the inner ear labyrinths of most Europeans and Africans. While the overall shape of the bony labyrinth differs between Asian and European populations, both groups tend to have slightly larger centroids than African populations. Furthermore, African populations exhibit less morphological variation in the bony labyrinth compared to European and Asian populations, contradicting the general perception of greater phenotypic variation in African populations. This finding warrants further investigation. The inner ear labyrinth morphology of later EMH fossils (Qihe, Zhaoguodong, and Longlin) fall within the range of variation observed in modern Asian populations. In contrast, earlier EMH fossils (Liujiang and Ziyang) exhibit similar bony labyrinth morphologies and share greater similarities with both European and Asian modern populations. Besides, early modern humans from Liujiang and Ziyang exhibit smaller bony labyrinth centroid size than other fossil hominins and modern populations. This suggests that these early EMHs may represent an initial morphology of the population before its divergence into European and Asian lineages following their entry into Eurasia.