This paper introduces the procedure and results of the dependence modeling for a complex supply chain management (SCM) system using the design structure matrix (DSM). The elements of the DSM are determined by the functional analysis of the overall SCM system. Population of the matrix results from utilizing the biperspective group decision method, which evaluates the degree of dependence between the influencing and the dependent components. More specifically, this is accomplished by separately eliciting the opinions of the two parties and systematically obtaining the converged assessment. A case study for dependence modeling of an SCM system of a leading aircraft manufacturer is presented. From the obtained model, we can better understand the cross-functional interactions among the components of an SCM system and corresponding behaviors. Thus, this paper analyzes the gaps between the degrees of dependence perceived by the two parties and provides some discussions on how the analysis results can be used to improve the operation of the system.