Abstract: This study focused on silver carp (Hypophthalmichthys molitrix) from the Three Gorges Reservoir area. By analyzing the differences of otolith microchemistry (trace elements Sr﹕Ca, Ba﹕Ca, etc., and stable isotopes δ¹³C and δ¹⁸O) in different populations, the indicator of otolith microchemical composition of silver carp on habitat environment was discussed, and key indicators leading to differences were screened. It provides a new technique for the study of habitat resume reconstruction of silver carp and the identification of wild population and breeding/release populations. Based on the otolith microelement data, relevant statistical analysis was carried out, and the results of discriminant analysis showed that the average success rate of discriminant for four sample sites of silver carp in the Three Gorges Reservoir area was 83.6%. One-way analysis of variance showed that Li/Ca, Na/Ca, Co/Ca, Sr/Ca, and Ba/Ca had significant differences among the four sample populations. The results of principal coordinate analysis showed that there were significant differences in the ratio of trace elements in otoliths of silver carp among different sample sites, and the index with the highest contribution rate of the first component was Sr/Ca (35.3%), Co/Ca (28.4%), and Ba/Ca (20.2%), which indicated that Sr/Ca, Co/Ca, and Ba/Ca were more suitable to be used as the key indicators for the habitat resume reconstruction study of silver carp. Based on the otolith isotope data, relevant statistical analyses were also conducted. One-way analysis of variance showed significant differences in δ¹³C and δ¹⁸O values among 6 populations. The δ¹³C and δ¹⁸O bitmaps showed that Taipingxi, Wanzhou, and Fengdu were grouped together, while Banan, Beibei, and Banan original seed farms were grouped together, which indicated that the sampled individuals in Banan may be from breeding and release to a certain extent. In summary, otolith trace elements Sr/Ca, Co/Ca, Ba/Ca, as well as the stable isotopes δ¹³C and δ¹⁸O, exhibit significant differences among different silver carp populations, which can be used as key indicators for habitat resume reconstruction study of silver carp. Additionally, the analysis of δ¹³C and δ¹⁸O value effectively distinguishes between wild and breeding/release populations.