In the view of engineering philosophy, the mining engineering is a dynamic operating process of ferrous material flow, in which the ferrous material flow is processed orderly through a series of continual coordinated procedures. It is also a process of discarding the dross, selecting the essential, and extracting the original metal. The object of management is to fulfill the multi-objective optimization. The proportion of lean ores in iron ore resources is 82% in the world and even 97% in China but their utilization is very low. Aiming at the bottleneck and weakness of China’s resource development, this paper analyzes and plans the mining engineering system as a whole based on the ideas and methods of system theory and engineering philosophical thinking. And the paper proposes the “grade decision-based multi-system integration” engineering management mode, which considers the relationship between engineering and environment and complies with the natural law. In the mode, the mining engineering, including geologic mining, ore blending, concentration and pelleting, can be viewed as a whole and the geological grade, mined ore grade, feed grade, concentrate grade and feed grade of blast furnace can be considered comprehensively. The mode reflected the overall structural optimization idea, realized the analysis, coordination and optimization among the multiple functions and processes, and thus drove the overall efficient and profit optimization throughout the processing flow. The establishment and the application of the “grade decision-based multi-system integration” mode have solved the lean iron ores exploitation problem and supported the “self-sufficiency” resource strategy.