In order to study the influences of defective rail welding joints on wheel/rail interaction, a transient finite element model of a high-speed train passing over rail welding joints is presented on the basis of field measurements. Focusing on the physical mechanisms differences of wheel/rail rolling contact on welding joints with varying rail straightness at rolling speeds of up to 400 km/h, this model takes vehicle/track system dynamics and wheel/rail elastic–plastic deformations into account. The defective thermite welding joint with short wave irregularity easily leads to rail nucleus flaw with residual stress. When the running speed is over 250km/h,the maximum value of wheel/rail vertical force at welding joint has a basic trend of a bilinear increase with the increase of running speed and the unevenness of the welding joint. There is a phase difference between the maximum contact force and the peak joint irregularity. When the high-speed railway operation management standard is 250~350km/h, the short wave irregularity at rail welding joint with over 0.3mm straightness should be grinded.