In complex system problems, a Decision Maker (DM) is often faced with choosing a subset of alternatives from a bigger set. This process is known as multiple criteria decision making (MCDM). Examples of MCDM include decision making in human resource management, water resource management, environmental management and site selection, energy policy issues, portfolio selection, transportation and routing selection, student admission. In general, there are several criteria that need to be satisfied; however, they are usually at least partly conflicting. In this study, we propose a pseudo-boolean approach for multiple criteria decision making on complex system problems. The computational results illustrate both robustness and attractiveness of this solution approach.