To deal with problems in synergetic development of coal-based energy engineering, this paper, guided by the philosophy of engineering, proposes the synergetic management philosophy of “factors coordination, systems synergy, dynamic optimization and three-dimension planning.” The paper also establishes the synergetic management system characterized by systems factor synergy, resource-environment synergy and systems boundary extension and supported by the “two-wheel driven” management innovation and technological innovation. In addition, the paper presents a multi-objective dynamic optimization model for energy engineering, designed based on Shenhua’s own engineering practice, to analyze Pareto optimal solution in three scenarios: best resource allocation, minimal environmental impact and maximal value creation. This provides important reference to synergetic development strategies and decision-making in engineering management.