In order to establish a finite element model for dynamic stress response analysis of large structure at local details，a consistent multi-scale modelling method of structural behaviour based on the substructure method was proposed. The local fine finite element model was treated as super-element by the substructure method，and the displacement constraint equation was established based on the interface virtual work balance principle. The coupling connection of multi-scale interfaces was then completed based on the displacement constraint equation coefficients obtained from iterative calculation. Taking the three-dimensional box section cantilever beam structure as example，the multiscale modelling was established using substructure method. The stress response was analyzed and compared with the multi-scale model based on the rigid region method. The results show that the static analysis stress field of the proposed method agrees well with the refined whole shell element model， especially the stress field near the multi-scale coupling interface. However，the multi-scale model based on the rigid region method has discontinuous stress transition and stress concentration at the interface coupling，which is different to the refined whole shell element model. In addition，the transient stress response of the method is in good agreement with the refined whole shell element model. The research result can be applied to analyze the dynamic stress response of the local key component of large structure.