The rapid development of marine concrete structures and the sharp shortage of freshwater resources contribute to the wide investigation of seawater-mixed ultra-high-performance concrete (SWUHPC). However, few studies have investigated the chloride ions (Cl) binding mechanism of SWUHPC. Herein, the chloride binding experiments and molecular dynamics (MD) simulation were carried out to reveal the physically and chemically bound Cl mechanisms of SWUHPC. The results of the experiments clearly demonstrate that the addition of silica fume (SF) led to a significant decrease in the capacity of Cl binding. Conversely, the incorporation of metakaolin (MK) resulted in a marked increase in the content of chemically bound Cl. Furthermore, it is revealed through MD simulations that the amount of physically bound Cl heavily depends on the Ca/Si ratio of C-S-H. A higher Ca/Si ratio results in a stronger electrostatic effect of the C-S-H surface on Cl, which increases the physical binding of Cl via Ca-Cl bonds. In addition, it is found that Al[6] and Ca in the interlayer region of C-A-S-H formed the main structure layer (CaAl(OH)) of Friedel's salt, and then chemically adsorbed Cl in the pore solution. These findings provide novel nanoscale insights regarding the physically and chemically bound Cl mechanisms of SWUHPC.