Due to environmental loads, mechanical damages, structural aging and human factors, civil infrastructure inevitably deteriorate during their service lives. Since their damage may claim human lives and cause significant economic losses, how to identify damages and assess structural conditions timely and accurately has drawn increasingly more attentions from structural engineering community worldwide. In this study, a fast and sensitive time domain damage identification method will be developed. To do this, a finite element model of a steel pipe laid on the soil is built and the structural responses are simulated under different damage scenarios. Based on the simulated data, an Auto Regressive Moving Average Exogenous (ARMAX) model is then built and calibrated. The calibrated ARMAX model is used to identify different damage scenarios through model updating process using clonal selection algorithm (CSA). The results demonstrate the application potential of the proposed method in identifying the pipeline conditions. To further verify its performance, laboratory tests of a steel pipe laid on the soil with and without soil support (free span damage) are carried out. The identification results of pipe-soil system show that the proposed method is capable of identifying damagein a complex structural system. Therefore, it can be applied to identifying pipeline conditions.