By analyzing the effect of friction modifier of rail top on the adhesion characteristics of wheel rail, it was found that the FM not only changes the coefficient of friction, but also changes the Kalker weighting factor, which is different from the conventional belief that only coefficient of friction is changed after the application of friction modifier. The dynamic performance of freight cars running in the rail with friction modifier was studied considering the effect of friction modifier on coefficient of friction and Kalker weighting factor. A vehicle model of freight car was established with SIMPACK software package, which included a car body, bolster, side-frame, axle boxes and wheel sets, and etc. The stability and safety of the vehicle were analyzed on the straight and curved rails with friction modifier. Calculation results show that the application of friction modifier can significantly improve the lateral stability of the car-body, but it has little effect on vertical stability. The derailment coefficient and wheel unloading rate will be increased slightly after the application of friction modifier, however, they are both within the safe range of national standard，and would not do harm to the operation safety.