Under the backdrop of reforms in the operational mechanisms of oil and natural gas pipeline networks and the objectives of “carbon peak and carbon neutrality”, the operational conditions of pipelines have become more variable and the transportation mediums more diverse, expanding the boundaries of pipeline transportation. However, this also introduces more operational risks and safety hazards, urgently requiring the resolution of scientific issues and key technologies for flexible transportation through complex networks. This article analyzes the essence of flexible pipeline transportation, identifies the challenges faced by different types of pipeline networks, and on this basis, summarizes the current development status and technical difficulties of key technologies in flexible pipeline transportation. Finally, from six key directions—open markets, safety protection, digital twins, transportation optimization, multi-network integration, and innovative applications—suggestions are proposed for the development of flexible pipeline transportation in China. These recommendations aim to provide more accurate guidance for energy planning and management, thereby helping to construct a low-carbon, flexible, safe, and efficient modern comprehensive energy system.