The true dynamic characteristics of dams, namely, natural frequencies, damping ratios, and mode shapes, are important to earthquake-resistant design. Thus, system identification based on in-site measurements is useful for numerical analysis and health monitoring. The well-instrumented strong motion array on an arch dam in Southwestern China recorded some seismic response data. The dynamic properties of the dam are identified from records of the top five strongest earthquake motions using power spectral density functions, transfer functions, and the ARX model. The identified modal parameters of the different seismic events are compared, and the stability of the stiffness of the dam system from 2002 to 2008 and the nonuniformity in the input ground motion are indicated. A linear finite element model of the dam and a nonlinear model that considers contraction joints are constructed and calibrated to reproduce the frequencies determined from the system identification. The modal analysis highlights potential information about the dynamic characteristics of the dam. The comparison of the results of the system identification and calibration shows that the use of the nonlinear model may be reasonable in simulating the dynamic response of the Ertan Dam.