Supply chain is an important key for any businesses’ existence and development, since this concept can be a solution for them to hold efficient operational practices, minimizing cost, and on time delivery. Therefore, appropriate management practices on supply chain of agricultural commodity could be a substantial matter since it has been facing problems in efficiency, supply, and minimizing cost. The higher the economic value of a commodity, the more important the role of management on its supply chain. One of Indonesia’s strategic and high valued commodity is shallot due to its high consumption and great contribution on regional economic development of production areas. Performance of shallot supply chain may impact on the parties involved, as farmers, traders, and suppliers. Thus, in order to formulate an accurate strategy to improve shallot supply chain performance, a measurement model is needed. This research employed Supply Chain Operations Reference (SCOR) method to identify the model, while analytical hierarchy process (AHP) was used to determine the weight of each indicator in the model. Findings of this research indicate that production is the key aspect on shallot supply chain. Furthermore, quality and order-fulfilment the most significant parameter in defining its performance is quality. Cost and order-fulfilment are proven as the highest weight-scores attribute and indicator, respectively, in measuring the performance of shallot supply chain.