It is recently recognized that the ore mineral system is a complex dynamic system, and that the mineralization is of a non-equilibrium and non-linear process. Based on this theoretic framework, the mineralization is primarily a physical process, and the mineral system is a fluid-driven geological sub-system. The magma system with small volume is also of a fluid-driven geological sub-system. Therefore, there exist instinct relations between the small intrusions and the endogenic mineral deposits, and revealing such relations is the key to practice the metallogenic theory in complex systems. The research shows that the theory of metallogeny by the small magmatic intrusion opens new windows for improving magma dynamics, and is one of targeting elements for the regional prognosis of mineral deposits and a milestone from which new departures in the economic geology would be started.