Eriocheir sinensis, the Chinese mitten crab, has decreased dramatically in the Yangtze Estuary in recent years. Distribution of mitten crab larvae in the Yangtze Estuary and the influence of oceanographic features on their densities were analyzed based the samples collected from 27 stations in March, April and May 2013–2015. Results showed zoeae I and II began to appear in March, zoeae III and IV in April, and zoeae V and megalopae in May. The spatial patterns of zoeae II, III and IV were identified as having a highly clustered distribution. Habitats located near the mouth of the North Branch were mainly hotspots of each stage larvae. Both biotic (zooplankton biomass) and abiotic variables (water temperature and depth) had significant impacts on the larval densities. Compared with 1986–1988, the original nursery habitats have moved approximately 20–50′E towards the shore, and have locally lost the nursery function after the Three Gorges Dam (TGD) construction.