Resource allocation is an important activity in planning of a product design process so as to achieve a desired result. Aiming at building a methodology of optimal resource allocation, this paper proposes a optimization method of DSM clustering operation for design structure analysis. The proposed method has two independent objective functions, i.e., expected performance and expected quality of designed product. The effect of resource allocation and milestones/options management is regarded in the objective functions. This paper demonstrates its application to a student formula car project, verifies the proposed method and discusses open issues.