Eriocheir sinensis is an important economic species in China. It is widely distributed in the Yellow River, Yangtze River, and other river basins in China. It exhibits distinct feeding migrations and reproductive migrations. However, since the implementation of a 10-year fishing ban in the Yangtze River, it has been difficult to obtain fishery data. Therefore, a new method for monitoring E. sinensis resources under the background of the fishing ban in the Yangtze River needs to be established to monitor megalopa resources during the flood season. In this study, eDNA technology was used to monitor the abundance of E. sinensis megalopae, which helped reveal the dynamic changes in the population size of megalopae in the Yangtze River estuary and monitor the resource status of E. sinensis. By establishing an indoor quantitative curve and collecting eDNA samples from the Yangtze River Estuary, combined with megalopa resource survey data, the distribution of E. sinensis megalopa resources in the Yangtze River estuary was elucidated. The indoor quantitative curve of megalopae in the four concentration experiments(with concentration gradients of 1 megalopa per 20 liters of water, 10 megalopae, 100 megalopae, and 1000 megalopae) within 72 hours had the best fit with a power function. After removing the larvae, the eDNA concentration in the water was negatively correlated with time, and the power function best represented the relationship between eDNA degradation and time, which was consistent with previous research results for other crustaceans. In June 2023, the average density of megalopae in the Beibayao waters was (23.03±55.10) ind/m³, and the eDNA concentration range was (9145.86±31147.36) copies/mL. There was a highly significant correlation between the density of megalopae and the standardized eDNA concentration, and the power function equation had the best fit. The density of megalopae monitored using a plankton net in the Tuanjiesha waters was (0.38±0.99) individuals/m³, and the eDNA concentration was (29808.3±95359.04) copies/mL. There was a time-lag effect between megalopae density and eDNA concentration in the Tuanjiesha waters, with changes in density preceding changes in eDNA concentration by 5 days. After the lag, the density of megalopae was correlated with the standardized eDNA concentration, and the best-fit equation was a linear equation. The main reason for the lageffect was that the migration speed of megalopae was faster than the water exchange speed; thus, the megalopae arrived at the Tuanjiesha waters before the eDNA they produced. This study demostrates that the current method of using eDNA technology to analyze E. sinensis megalopa resources is only applicable to waters close to the occurrence of the megalopae.