With the continuous development of aerospace industry, the load transfer structure of spacecraft is getting more and more complicated. In practical engineering, how to distribute the loads in a reasonable way is of great significance for the lightweight design of spacecraft and the guarantee of structural load carrying capacity, and it is also necessary to take into account the non-ideal boundary conditions of the overall structure to the local structure in the process of dynamic load transfer structure design. Based on this, this paper proposes a dynamic topology optimization design method for dynamic load transfer structure based on structural boundary condition equivalence, which can fully consider the influence of the overall structure on the local structure while designing the load transfer structure. The method firstly simplifies the connection boundary between the local structure and the overall structure into a spring unit and a centralized mass unit, optimizes the unit parameters through genetic algorithm to achieve the equivalence of boundary conditions, and finally establishes a topology optimization model of the load transfer structure based on the unit density variable in conjunction with the design objective of the dynamic compliance of the structure. Numerical examples verify the effectiveness of the new method and obtain the optimization design results with the variation of volume fraction, external load frequency and load constraint interval.