In this paper, a novel model updating method for the vehicle/track system in the subway is put forward. Present study indicates that the train speeds and fastening system stiffness are two key issues dominating the model updating process of the track subway system. For demonstration, a vehicle/track coupling model based on the multi-body system is presented and the dynamic response of track system subjected to the moving train is computed using an iterative method. Then, a typical subway track in service is selected for the present investigation to capture field testing data. The numerical predictions of the dynamic response of track computed by the proposed model updating method are verified and compared with the field testing results. The following conclusions are drawn: (1) the fastening system stiffness plays a more dominating role in affecting the dynamic response of the track than that of the fastening system damping; (2) updating the running speeds can influence the major excitation frequencies of running vehicle on the tracks, which may produce more consistent results referred to as field measurement; (3) updating fastening system stiffness may result in denser distribution of frequency amplitudes; and (4) the spectrum of rail displacements is dominated by n times of the first order train loadings since the effects of multiple supports on the track structures are taken into account.