The interface properties of Fe(101)/zinc silicate modified by organo-siloxane (KH-570) was studied by using the method of molecular dynamics simulation. By calculating the temperature and energy fluctuation of equilibrium state, equilibrium concentration distribution, MSD of layer and different groups, and interaction energy of two interface models, the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale. It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage (t < 20 ps). It can be seen from the multiple peak states of concentration distribution that the iron substrate, organo-siloxane and zinc silicate are distributed in the form of a concentration gradient in the real environment. The rapid diffusion of free zinc powder in zinc silicate coating was the essential reason that affected the comprehensive properties of coating. The interface thickness decreased from 7.45 to 6.82 Å, the MSD of free zinc powder was effectively reduced, and the interfacial energy was increased from 104.667 to 347.158 kcal/mol after being modified by organo-siloxane.