This paper proposes an efficient dynamic modeling and control framework for variable configuration spacecraft during payload separation or docking. A variable topology matrix is devised to address abrupt changes in mass, static moment, and inertia changes caused by structural reconfigurations, ensuring smooth parameter transitions. An integrated adaptive sliding mode control (ASMC) system with a modal observer is proposed to address inertia uncertainties and flexible panel vibrations. The modal observer reconstructs unmeasured vibration modes in real time, while the ASMC employs dynamic control gains to counteract modeling errors and parameter drifts. Lyapunov stability analysis strictly confirms closed-loop system stability under all specified uncertainties. Numerical simulations demonstrate the effectiveness of the approach through fast attitude stabilization, significant vibration suppression, and smooth topology transitions. This research offers a systematic method for managing coupled rigid-flexible dynamics in variable configuration spacecraft, improving mission reliability through better adaptability and precise control. The proposed framework significantly enhances the adaptability of spacecraft to dynamic environments and provides a more accurate and reliable control performance, which is crucial for the success of space missions.