The motivation of this article lies in the application of two-stage gap-based measurement (GBM) in supply chain management. It adopts GBM model to construct a mixed integer program to measure the various stages of supply chain management in manufacturing practice. This paper proposes a new assessment system that aims to measure the aggregated efficiency of the entire supply chain. In this system, “plan source” and “plan make” are the major elements, they are a widely accepted industry standard by Supply Chain Operations Reference (SCOR). “Plan source” emphasizes the assessment of demand/supply planning strategy and suppliers’ performance; “plan make” emphasizes the shop floor control, profitability and equipment effectiveness. The resulting GBM scores provide complete information on how to project inefficient DMUs on to the frontier. This article continues with a demonstration of GBM in the company cases, for the results of the assessment; this paper finds the worst efficiency of the DMUs and proposes improvement programs.