Donor milk from the human milk bank is important for vulnerable infants without their mothers’ own milk. Longitudinal changes in toxic metals in donor milk has not been reported. This study aimed to assess the effect of donors’ demographic characteristics, life habits and dietary habits on the concentration of metals in breastmilk donated to a human milk bank and to assess the health risk of lead (Pb) and mercury (Hg) exposure of donor mothers’ offspring through breastfeeding and the vulnerable recipients. A total of 228 samples, which were longitudinally donated to the human milk bank by 39 donors, were selected specifically to assess the levels of Pb, Hg, and MeHg. Donors’ offspring were also enrolled as mother-infant-dyads to monthly obtain the milk consumption and body weight. The results showed significant differences in the infant risk in exclusive breastfeeding months. The average Pb level of breast milk was 6.49 ± 5.23 µg/L (mean ± standard deviation), and the Hg level was 0.76 ± 0.98 µg/L. The sources of these toxins—residential districts, cleaning products, cosmetics, drinking water, viscera, eggs, seafood, and canned food—have a significant influence on the concentration of toxic metals in human milk. This study showed an unacceptable non-cancerous health risk (95th percentile hazard index, HI = 1.37 > 1) for Pb and Hg. In the future, the breast milk offered by the bank should be strictly monitored, especial for Pb, to ensure high-quality donor milk for vulnerable recipients but also donor mothers’ offspring who depend on it. Graphical Abstract