Space transportation systems have supported China in completing numerous major space engineering projects, including manned spaceflight and lunar exploration missions. Facing the intense demands for future launches and the necessity of scheduled space transportation, there is a growing need for launch vehicles with higher development efficiency, greater adaptability, and improved comprehensive performance. Control technologies can play a significant role in this development process, and continuously innovating at the theoretical method level is a very cost-effective solution compared to other technical approaches. The paper highlights three key challenges in space transportation system control technology: the integrated design of guidance and trajectory planning, strong adaptive control in the face of global uncertainty, and active flow pattern control in cryogenic fluid transmission. For the first two technologies, their conceptual connotations, necessity, research and application status in the Long March launch vehicles, and future prospects are discussed. For the third technology, a technical roadmap for autonomous control based on multidisciplinary crossover solutions is proposed. These challenges have long been neglected due to the lack of good solutions, which has limited the further improvement of launch vehicle performance. With these technological breakthroughs, we anticipate a significant advancement in space transportation systems.