Metamorphic mechanisms have attracted considerable attention owing to their capability to switch their topology to adapt to different operational tasks. One feature of topological change is the re-contact of different bodies, which inevitably causes collisions affecting operation accuracy and service life. Consequently, in this study, a collision incidence matrix was introduced to describe the topology of a system involved in collisions, and a method for reducing the closed-loop system to an open-loop system was proposed. The complex movement of the metamorphic mechanism in a changing topology was classified into two different running stages of the source metamorphic mechanism. Based on the relative coordinate method, dynamic modeling of the source metamorphic mechanism considering the impact effects was conducted. Combining the classical collision theory and Newton–Euler equation, the generated impact impulse and the motion after collision were determined. Subsequently, a dynamic analytical method for the full configuration of metamorphic mechanisms was proposed to reflect the changes in the topological structure in the dynamic model. Finally, two typical metamorphic mechanisms used in packaging and spinning were considered as examples to verify the correctness and effectiveness of the proposed method, and their impact characteristics during configuration transformation were analyzed. The proposed analytical method of internal impact for a variable topology process provides effective theoretical guidance for the stability analysis of configuration transformation and structural design aimed at minimizing impacts.