Identifying the main factors on spatial differences in net growth rate of Yesso scallop ( Patinopecten yessoensis ) in culture system is the key to effective aquaculture management and development. Coupling a 3D ecosystem model (ROMS-CoSiNE) with a dynamic energy budget model for scallops, a Yesso scallop culture ecosystem (YeSCE) model was established with which scallop growth was simulated with real seeding density and juvenile size from local aquaculture experiments from December 1, 2012 to November 30, 2013. Results show that the YeSCE model has reasonably simulated the environmental variation and scallop net growth rate in the Changhai sea area. The growth of scallops was slow in winter and midsummer and was limited mainly by temperature. Food availability was a key factor that contributed to the fast growth of the scallops during spring to early summer and in autumn. Generally, the scallops cultured in the north part of the Changhai sea area grew faster than those in the south; and the net growth rate for scallops cultured near the island was significantly higher compare to the others, which is probably correlated to the spatial distribution of food availability. Based on the correlation analysis, the spatial differences of the net growth rate were largely affected by the length of the match timing of temperatures and food availability. The results of this study provide a scientific support for optimizing bottom culture planning and adjusting bottom culture methods.