Abstract: Based on the basic concept of the generalized response displacement method， a dynamic sub-structure analysis method suitable for the longitudinal seismic response of a shield tunnel crossing longitudinally uneven sites is proposed. An explicit parallel calculation model of the longitudinal uneven free field and a three-dimensional （3D） refined explicit parallel calculation model of the surrounding rock-shield tunnel system are established by using the newly proposed sub-structure analysis method. The real-time transmission of dynamic deformation between the two models on the boundary is achieved through the sub-structure method. The free-field seismic wave at the buried depth of the tunnel is transformed into the equivalent earthquake action of the surrounding rock-shield tunnel sub-structure model. Compared with the traditional beam-spring model， the model method in this paper can achieve the 3D refined simulation of the surrounding rock-tunnel system and the longitudinal non-uniform ground motion input along the tunnel caused by the site seismic effect. The reliability of the model method in this paper is verified by comparing it with the calculation results of the 3D refined analysis model of the shield tunnel. The results show that the model method in this paper has a clear concept， simple modeling， low calculation cost and small differences in results， which can fully reflect the longitudinal seismic response of shield tunnel crossing longitudinal uneven sites. It provides a more efficient analysis method for the longitudinal seismic design of shield tunnels crossing longitudinal uneven sites with soft-hard connected media.