The aim of this study was to further explore a convenient and feasible method to assess the fishery resources correctly and conveniently using the eDNA technology for the large yellow croaker (Larimichthys crocea). Under the comparison with the result of bottom trawling fishery survey, two eDNA methods (metabarcoding and real-time qPCR) were used to investigate the biomass and distribution of the large yellow croaker in autumn and spring seasons in the central and southern regions of the East China Sea. The results suggested that the designed NADH2 specific primers and developed real time qPCR method were more applicable and reliable. The variation of eDNA concentration of large yellow croakers well coincided with the one of real capture survey in the East China Sea. And the difference of eDNA concentration between in surface and bottom water samples reflected the distribution characteristics in water layer related to life history of L. crocea in two seasons. The developed method based on eDNA technology and real time qPCR method not only could be used to evaluate the resource distribution, but also could contribute to estimate the life history and migration route of large yellow croaker.