In this paper, a novel composite sandwich structure analysis of Launch Vehicle (LV) fairing is considered and proposed by a new Multidisciplinary Design Optimization (MDO) for a two-stage launch vehicle. Accordingly, “Multidisciplinary Design Optimization based on Independent Subspaces” (MDOIS) is employed using the “Fixed Point Iteration” (FPI) method to achieve the best convergence at system level (SL) to segregate the disciplines. Therefore, two proposed subspaces overcome difficulties of common mentioned MDO of LVs. Hence, the first subspace is a MDO which includes propulsion, aerodynamics, weight and trajectory disciplines and the second one, includes the novel composite fairing structure optimization as the other single discipline optimization that considered as a compact problem analytically and numerically and it is one of the novelties of this work. By considering variables as propulsion, trajectory and also composite sandwich fairing structure design regarding to the variables of designing and the performing optimization process, the fairing mass has been reduced more and considerable with respect to the common two stages LVs. In addition, due to the global optimization of LVs this weight reduction caused in reduction of the total gross weight of LVs. This system engineering proves the high sufficiency of MDO in complicated designing and it can be a roadmap for the future space vehicles designers especially who want to consider the composite structure optimization in LVs. Manuscript profile