An algorithm for predicting the perturbed trajectories in a multi-machine system is proposed based on an additional virtual node. Through an on-line analysis of the perturbed system and the data on the state estimation or power flow， the power system is reduced in order to a system of reserved nodes of power plants with only PMU. By introducing an additional virtual node， the variety of system elements' model or their parameters and alteration of the network topology can be identified by mutual admittance between the virtual node and reserved node. The mutual admittance can be modified based on the PMU data. Using the transitive relationship matrix between the voltage and current of the reduced-order system， the perturbed trajectories prediction should be realized by the connection model between generator equation and network. The effectiveness of the proposed algorithm is verified with numerical simulation on a 10-machine 39-bus power system， with the resultant scheme implemented.