E. sinensis, normally harvested in October and November, is an economic aquatic product in China. Pond culture has been widely applied for the production ofE. sinensis, wherein a stable food supply for crabs is provided. In order to improve the nutritional quality ofE. sinensisproducts, this study evaluated the effect of the local pond culture on the nutritive profiles ofE. sinensisand screened out the best harvest time for the nutrient-rich crabs, thereby guiding the local crab industry to improve its aquaculture mode and harvest strategy. The results indicated that pond culture enhanced the levels of protein, amino acids, and specific organic acid derivatives, and reduced the levels of peptides and polyunsaturated fatty acids (PUFAs). Compared withE. sinensisharvested in October, peptide levels were significantly increased, whereas sugar, phenolic acid, and nucleotide levels were decreased in those harvested in November. Overall, the study revealed that the nutritive profile of the pond-rearedE. sinensiswas significantly modulated by a high-protein diet, thus lacking the diversity of metabolites. Additionally, October could be more appropriate for harvestingE. sinensisthan November.