Abstract: The multilevel hierarchical engineering structure system is defined as a structural series of multilevel branching and general distribution of structures, that is characterized by main engineering structures in a complex construction project of functionally logical relationships. Under the engineering background of multilevel aseismic design and the case where structural earthquake fortification intensities are used as variables, programming models for the global optimization of the system are established in this paper. Meanwhile, two levels of global optimization methods, including a hierarchical condensation method and two modified minimizing approaches, are put forward to overcome the discreteness of objective functions as well as the complexity of the system. The former is employed for the analysis of system modeling; and the latter, with a modified conjugate gradient method and a modified Lagrange direct method, is utilized to evaluate unconstrained and constrained minimization, respectively. An example is presented to demonstrate the optimization of the near-optimum earthquake fortification criterion, construction cost, and allocation of total investment of a complex construction project. Concepts, principles and methods proposed in this paper can provide a basis of theoretical analysis of the systematized design of complex construction projects, and the scientific decision-making in civil engineering as well.