Currently, space-based information networks, represented by satellite Internet, are rapidly developing. UAVs can serve as airborne mobile terminals, representing a novel node in satellite IoT, offering more accurate and robust data streaming for connecting global satellite–UAV collaborative IoT systems. It is characterized by high-speed dynamics, with node distances and visibility constantly changing over time. Therefore, there is a need for faster and higher-quality topology optimization research. A reliable, secure, and adaptable network topology optimization algorithm has been proposed to handle various complex scenarios. Additionally, considering the dynamic and time-varying nature of these types of networks, the concept of time slices has been introduced to accelerate the iterative efficiency of problem-solving. Experimental results demonstrate that the proposed algorithm is expected to exhibit better convergence and performance in subsequent iterations compared with traditional solutions. Besides being a solution for topology optimization, the proposed algorithm offers a new way of thinking, enabling the handling of larger satellite–UAV collaborative IoT systems.