The final architecture of a complex system reflect preferences of several value chain stakeholders on system attributes, also called “ilities”. Owing to differences in their individual roles and responsibilities, different stakeholders prefer different approaches to architect and decompose a system to optimize their attributes of interest. However, owing to increasing complexity of modern engineering systems, optimizing multiple attributes of complex systems has become challenging; moreover, very few researches have been published in this regard. Thus, to address this gap in available literature, this paper presents a multi-attribute optimization framework for complex system decomposition. The proposed framework primarily optimizes two attributes—system robustness (to the perspective of the stakeholder), and modularity—while system maintainability is considered an optimization constraint. Feasibility of the proposed framework has been demonstrated through a case study, wherein system attributes of three different mechanical clock models having different architectures were optimized.