Aiming at the problem that the longitudinal modes of structural system of rocket need to be identified from its integral modes in engineering, a method that automatically identifies the longitudinal modes of structural system of rocket was proposed according to the theory of modal effective mass. Taking the vibration characteristics of system with lumped mass as a computing example, applying the finite element software, the beam model of system with lumped mass was established, and the longitudinal modes of the system were automatically identified based on the method. Compared with the system modal information calculated by the method of modal analysis, this automatic identification method not only can accurately identify the longitudinal modes of vibrating system, but also has automatic and high efficiency identification feature. It provides a theoretical basis for the dynamic model of POGO vibrating system in liquid rockets and other model of engineering systems to be accurately and promptly established.