Seawater desalination is widely used to overcome the freshwater shortage worldwide. However, even after three-stage reverse osmosis treatment, the desalinated water still contained 14.6 μg/L of aliphatic disinfection byproducts (DBPs), 384.2 ng/L of bromophenolic DBPs, 3.5 ng/L of iodophenolic DBPs, 1024.7 μg/L of Br-, 2.8 μg/L of I-, and 2.4 mg C/L of dissolved organic carbon (DOC). After the desalinated water was disinfected with chlor(am)ine, the concentrations of halogenated aliphatic and phenolic DBPs further increased, and bromophenolic DBPs were the toxicity forcing agents. When surface water was mixed with desalinated water and then chlorinated, the yield of aliphatic and phenolic DBPs significantly elevated. Separately chlorinating desalinated water and surface water before mixing could mitigate this adverse situation. Chloramine disinfection was more conducive to reducing the total calculated toxicity of disinfected desalinated waters and mixed waters compared to chlorine disinfection. The treatment of desalinated water with granular activated carbon could effectively remove DOC and UV254, leading to a reduction in the content of total organic halogen after chlor(am)ination. Although anion exchange resin could adsorb Br-, it also released the organic precursors of DBPs, ultimately increasing the yield of DBPs. The results of this study can provide a reference for the seawater desalination industry to improve seawater pre-treatment and desalination processes and thus minimize the DBPs.