<p>Rapid urbanization in China is closely related to the contributions of the migrant population. Dongguan, a megacity located in the hinterland of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), has the highest proportion of the migrant population to total population of all cities in China, and this has affected the industrial layout and the supplies of local public services. However, the mechanism influencing the spatial distribution of the migrant population in the hinterland of the GBA is underexplored. On the basis of the Dongguan Subdistrict and Township Yearbooks, migrant population data from 2021 were obtained at the community/administrative village level. Spatial autocorrelation analysis was used in combination with a geographic detector to explore the distribution characteristics and causal mechanisms of the migrant population. The results show that (1) the spatial distribution of the migrant population in Dongguan city varies significantly, revealing a distribution pattern of agglomeration along the administrative boundary of the Shenzhen Special Economic Zone and spatial mixing between urban and rural areas. (2) The “net operating incomes of grassroots governance units”, “total numbers of various types of enterprises”, and “number of industrial enterprises” have high explanatory power regarding the spatial agglomeration of the migrant population. The study shows that the flat governance structure and economic model of Dongguan together contribute to the dynamic changes in its economic and social development, but this megacity also faces the challenge of sustainable development. This study therefore provides theoretical support and policy suggestions for spatial planning and social governance.</p>