This article studies the construction methodology of systems engineering for complex aviation products. With the growth of the complexity of aviation product development, aviation-manufacturing enterprises in China expect to apply the methodology of systems engineering in their development processes to improve the development capability for complex products. To solve this problem, a four-layer architecture is proposed, which includes request layer, process layer, method layer, and operation layer. Through this architecture, top-level regulations and requests can be decomposed and refined layer by layer, and then transformed into practical operations. In addition, some key problems that may arise in the system construction of systems engineering were also discussed.