The natural, economic, and social attributes of mineral resources determine that the security of mineral resources involves numerous resource types, large spatial distribution, ultra-long industrial chains, huge industrial scale, spatial and temporal configurations, complex factors, and multiple levels; it is a complex and giant system with a large scale, multiple levels, and complex influencing factors. How to make this system operate efficiently and serve economic and social development is a complex scientific issue. This study puts forward a concept of giant system for mineral resource security by introducing the research idea of system science, depicts the structure and composition of the giant system, and reveals the driving mechanism of the giant system by natural resource, economic, social, and other factors. On this basis, a new research direction of system engineering of mineral resource security is established, which involves building a theoretical knowledge model for mineral resource security guarantee using a system thinking, constructing a simulation experiment system based on a big data platform, and actively promoting government decision-making and feedback. Furthermore, a major strategic idea of establishing an overall design department for mineral resource security is proposed. The research results have been applied to and effectively supported national resource security guarantee in China.