This article is aimed at demonstrating how multidisciplinary design optimization (MDO) can be effectively applied to the preliminary design of an unconventional configuration aircraft, using the flying wing configuration aircraft as an example. Based on the two-level optimization method, a procedure is proposed for the implementation of MDO of the aircraft preliminary design, which consists of three main parts: system level optimization, subsystem level optimization (or evaluation) and multidisciplinary model generator. The objective of the system level optimization is to obtain overall optimal performance through the adjustment of the global design variables. The subsystem level consists of several disciplines, including aerodynamics, stealth, structure, internal layout, mass and performance. The task of the subsystem level optimization is to optimize the design goal of each discipline under the discipline constraints by the adjustment of local shape design variables. A multidisciplinary model generator is used to generate automatically a model for each disciplinary analysis, and it is one of the key techniques enabling the automation of the MDO process. A computing framework which integrates all the disciplinary analyses and optimization models is established based on the proposed MDO procedure. The application example indicates that the MDO procedure proposed in this article can be applied effectively to the preliminary design of an unconventional configuration aircraft.