The design of engineering systems often involves multiple disciplines and competing objectives, which requires coordination, information exchange and share amongst the disciplines. However, in practical design environments, designers have to make decisions in isolation due to organization barriers, time schedules and geographical constraints. This paper will propose a new approach for the multi-objective multidisciplinary design optimization (MDO) problems in non-cooperative environments based on gene expression programming (GEP) and Nash equilibrium in the game theory. In this approach, the GEP method is used as a surrogate to construct the approximate rational reaction sets (RRSs) in the Nash model. The effectiveness of the proposed method is demonstrated by the design of a thin-walled pressure vessel and the hull form parameter design of a small waterplane area twin hull (SWATH) ship. The results show that this approach can fully explore and provide the explicit functional relationship between the strategy of an isolated player and the control variables of the other players, thus able to obtain a better Nash equilibrium solution.