Abstract: As highly social animals, Indo-Pacific humpback dolphins (Sousa chinensis) exhibit community differentiation. Nevertheless, our understanding of the external and internal factors influencing these dynamics, as well as their spatiotemporal variations, is still limited. In the present study, variations in the social structure of an endangered Indo-Pacific humpback dolphin population in Xiamen Bay, China, were monitored over two distinct periods (2007–2010 and 2017–2019) to analyze the effects of habitat utilization and the composition of individuals within the population. In both periods, the population demonstrated a strikingly similar pattern of social differentiation, characterized by the division of individuals into two main clusters and one small cluster. Spatially, the two primary clusters occupied the eastern and western waters, respectively, although the core distribution area of the eastern cluster shifted further eastward between the two periods. Despite this distribution shift, the temporal stability of the social structure and inter-associations within the eastern cluster remained unaffected. A subset of 16 individuals observed in both periods, comprising 51.6% and 43.2% of the population in each respective period, emerged as a foundational element of the social structure and may be responsible for sustaining social structure stability, especially during the 2007–2010 period. These observations suggest that the composition of dominant individuals, an internal factor, had a more substantial influence on the formation of the social network than changes in habitat use, an external factor. Consequently, the study proposes distinct conservation measures tailored to each of the two main clusters.