The work aims to develop a multi-scale collaboration (MSC) modeling and simulation methods for massive model simulation to obtain the dynamic response characteristics of complex structure in transportation collision accidents, which benefits the safety evaluation of structure under dynamic loading. A finite element model including transportation vehicle, packaging container and complex structure was built by the developed multi-scale collaboration modeling method according to the actual shape and size of structures. Based on the developed method, numeric simulations were conducted on complex structure protected by packaging containers in truck collision accident and high speed train collision accident. The motion, deformation and damage characteristics of the overall system and key components were analyzed. Numerical simulation results, such as the motion process of the overall system as well as the deformation and damage of the inner structure, were in good agreement with experimental results both in truck and high speed train collision accidents, verifying the accuracy and practicality of the finite element modeling and analysis method. The developed multi-scale collaboration modeling method effectively addresses challenges in complex structure impact response analysis, including multi-geometry-scale, multi-time-scale and multi-scale nonlinear complexities and provides effective support to the analysis of the dynamic safety of complex structure in transportation collision accidents.