To determine the effects of growth and metabolism on carbon stable isotope turnover rates and fractionation factor of juvenile Eriocheir sinensis and different tissues, the hepatopancreas, muscle and gill tissues of juvenile E. sinensis in EA group [(4.0 g ±0.5) g] and EB group [(15.5 g ±0.5) g] were collected at 0, 7, 14, 21 and 28 days, respectively, in an aquarium of 0.2×0.2×0.3 m. The turnover process of stable carbon isotopes was investigated, and the fractionation factor of stable carbon and nitrogen isotopes were determined. The results showed that (1) The turnover rate of carbon stable isotopes in EA group was greater than that in EB group, and the turnover rate decreased with the increase of juvenile crab size. (2) The turnover rate of hepatopancreas was the fastest, followed by muscle and gills. The half-lives of hepatopancreas, muscle and gills in EA group were 20.88, 29.37 and 34.14 days, respectively, and those in EB group were 21.73, 35.18 and 66.01 days, respectively. (3) Metabolism was more principal for driving the turnover of carbon stable isotope with the contribution ranging from 79.82% to 94.04% for hepatopancreas, from 67.00% to 81.90% for gills, and from 71.61% to 90.36% for muscle. (4) The fractionation factors of carbon and nitrogen stable isotopes were 0.98‰ ±0.19‰ and 3.01‰ ±0.02‰, respectively. This study not only provided a reference for the nutritional ecology of juvenile E. sinensis, but also provided a scientific basis for bait selection in the breeding process of E. sinensis.