Desalination of seawater is an effective way to alleviate the world’s water shortage. However, the transmission and health risk of trace metals in the different processes of seawater plants are highly uncertain. Here, we investigated the concentrations of 29 ions and trace elements in desalinated water based on two desalination techniques – multiple effect distillation (MED) and reverse osmosis (RO) – and evaluated the potential health risks (carcinogenic risk (CR) and non-carcinogenic risk (n-CR)) of trace metals in these processes. The results showed that most ions and trace elements were efficiently removed using both the RO and MED methods. After desalination, the trace metal concentrations in the desalinated water treated with the MED method were higher than those in the desalinated water treated with the RO method. The n-CR values for the trace metals in the desalinated water using the MED and RO methods were within the neglectable level. The CR values based on the two methods were lower than the maximal acceptable risk levels designated by the US Environmental Protection Agency. The total health risks using the MED method were higher than those using the RO method. Our results indicated that seawater desalination using both treatment methods is safe.