Electrolysis of molten anhydrous magnesium chloride is an efficient way to prepare magnesium. Nowadays, it is still an attractive issue to reduce the production cost of anhydrous magnesium chloride in preparing magnesium process by electrolysis. This work focused on the local structure and transport properties of MgCl2 molten salt with impurity water system under various temperature conditions based on the first principles molecular dynamics simulations. The radial distribution function, coordination number distribution, angular distribution function, static structure factor, and self-diffusion coefficient in the temperature range from 1000 K to 1400 K, were compared with of pure MgCl2 to elucidate the microscopic interaction mechanism of impurity water. Besides, this study indicated that the first principles molecular dynamics simulation can serve as an effective and promising tool for the theoretical study of more complex molten salts and provide basic guidance for the experiment to fill in the gaps.