Abstract: To reduce the "Deviation between Price and Value (DPV)" of the value carriers of the medical value chains, and to achieve formal knowledge expressing and reconstructing, from the view of value "forming-flowing-obtaining-realizing" processes, a closed loop model is constructed for analyzing the medical value chain system. Based on this model and S-BOX model, the medical value chain system structures and operation mechanisms are respectively transformed into ontology structure bills and semantic rules, and then the S-BOX based reconfigurable medical value chain system knowledge model is constructed. Furthermore, the reasoning results denote that the DPVs of medical value chain nodes can be effectively calculated. And then with the DPVs, the value chains can be improved and reconstructed for controlling the pharmaceutical price intelligent.