[Objectives] This study aims to assess the risks of heavy metal pollution and long-term biological accumulation faced by the habitat of Alligator sinensis. In May and October 2021, heavy metal concentrations in water, soil sediments, feed for captive A. sinensis, and hatched eggshells were tested in eight sample areas within the National Nature Reserve of Chinese Alligator in Anhui Province. Among these, the Xiadu area hosts a captive population, while the Zhu Village, Gaojingmiao, Yanglin, Hongxing, Shuangkeng, Zhongqiao, and Changle areas harbor wild populations. The research focused on seven elements:mercury (Hg), cadmium (Cd), copper (Cu), zinc (Zn), chromium (Cr), arsenic (As), and lead (Pb). [Methods] The pollution levels in water and sediment contamination were evaluated using the comprehensive pollution index (R) and the Muller index (Igeo). Independent samples t-tests were used to analyze the differences in heavy metal concentrations between the environmental samples from May and October. To minimize harm, hatched eggshells were utilized to investigate heavy metal bioaccumulation instead of live individuals. The biological enrichment coefficient (BCF) indicated the accumulation of heavy metals from the environment, while the biological magnification coefficient (BMF) represented accumulation through the food chain. [Results] 1) Significant differences were observed in the concentrations of As, Cu, and Zn between the water samples from May and October (Table 1). In comparison to October, As and Zn concentrations were higher in May, while Cu concentrations were lower during that month. The comprehensive pollution index indicated that the water environment was free from heavy metal pollution (R < 1). However, the concentration of Hg exceeded the “Environmental Quality Standards for Surface Water,” suggesting that Hg poses a potential threat. 2) Significant differences were also noted in the concentrations of Hg, Zn, Cd, and Cr in the sediment between May and October (Table 2). Compared to October, Hg and Zn concentrations were higher in May, whereas Cd and Cr concentrations were lower. Specifically, Cd was non-polluted in May and increased to moderately polluted levels in October (Igeo = 1.56). Meanwhile, Hg exhibited slight pollution in both May (Igeo = 0.77) and October (Igeo = 0.30) (Fig. 1). 3) Concentrations of Cr and Pb in the eggshells exceeded the standards, with higher levels recorded in the Xiadu area compared to other areas (Table 3). 4) The BCF values for Cu and Zn in the water from the Xiadu area ranged from 2.05 to 38.61 (Fig. 2a), while all eggshells did not accumulate heavy metals from the sediment (Fig. 2b). The BMF values for As, Cu, Zn, and Cr in the feed ranged from 1.26 to 4.64. [Conclusion] This study showed that Cu and Zn were effectively accumulated in A. sinensis eggshells through the water environment. Additionally, captive populations were able to accumulate heavy metals through the food chain. Long-term accumulation of Pb in soil sediments may have led to excessive Pb content in eggshells. The study found that heavy metal concentrations in eggshells of captive populations were higher than those in wild populations. Bioaccumulation from both the environment and the food chain may have already negatively affected the reproduction of A. sinensis within the reserve. Therefore, it is essential to control Hg and Cd pollution sources and to improve the safety of the feed.