Researches on the dynamic properties and vibration modes identification of Printed Circuit Board(PCB)loaded on train are important for the train safety in transportation. In this paper, a novel approach to identify the vibration modes of PCB is presented. The free acceleration response of the PCB is expressed as the sum of linear exponentials, the zeros and residues of the free response are identified by the Prony method, the zeros and residues are optimized by the nonlinear total least 1-norm method. An experiment system is formulated to record the free response of PCB, the zeros and residues are identified and optimized, the simulation results indicate the approach presented in this paper is accurate to identify the PCB vibration modes. The algorithm presented in this paper is more robust and more accurate to identify PCB vibration modes. The technique in this paper is useful for PCB design and the safety management of train.