組織在營運過程中，為尊重其利害關係人之權益及健全組織之經營，須以良好內部控制制度為基礎，來強化組織管理機制，醫療機構如同一般企業在面臨醫療市場轉變，及全民健保制度衝擊下，其醫療服務品質及管理績效之良窳，日益受到重視。 醫療機構屬非營利事業，但若長期處於虧損，恐將無法永續經營，為能達到永續經營目標，醫院管理者應推動並落實「內部控制制度」，保障機構免於因人為缺失而造成損失，並降低錯誤與舞弊發生之可能性，以增進工作效率，維護財物安全，如此便可實現經營理念，亦可降低經營管理風險。 本研究選擇某公立醫院為研究對象，以本體論為方法，建構與設計其本體圖，診斷其內部控制制度，及檢視其醫院治理機制，並運用平衡計分卡強化內部控制機制，解決組織存在之部分問題，進而健全醫院治理機制。 本研究結果發現個案醫院嘗試以平衡計分卡解決內部控制機制執行過程，發現其遭遇些許挑戰，例如：各科部室對內部控制制度不熟悉、教學研究單位無成本觀念、公家體系公務人員抗拒心態、制式化之法規，及行政部門比醫療部門難以訂定目標與指標等。 儘管有些許挑戰尚待克服，但對於長久獨立於市場運作之公立醫院而言，平衡計分卡不失為一有效檢視組織與環境互動關係，並整合組織各部門運作，以進行資源配置之工具。 In order to respect the stakeholders’ rights and to better integrate management, Internal Control is emphasized to assist the organization’s management systems during operation. Healthcare institutions are facing market changes just as any general enterprise. The intersection of the National Health Insurance System, the healthcare service quality and management effects are presently of concern. Healthcare institutions are non-profit businesses. If any business encounters long-term deficit problems, it may become insolvent. To maintain sustainable management targets, the hospital administrator should put an Internal Control System into effect. Such an implementation will protect the institution from loss caused by human error and reduce the possibility of errors and dishonesty. In addition, it promotes work efficiency, increases safety and can lead to not only good management but also reduce management risks. The research chose a public hospital as the study object. It uses an Ontology Approach as the study method to construct and design the blueprint and to examine the Internal Control Systems and the Hospital Governance System. In order to solve problems in the organization and enforce a Hospital Governance System, it is effective to put the Balanced Scorecard into effect. The results of this study pointed out some challenges upon trying to implement the Internal Control system. Some of these challenges consist of unfamiliarity in departments, no cost consciousness in continuing education and research, resistant attitudes in government officers, standard legislation, and difficulties formulating goals and norms. Many public hospitals have long been excluded from healthcare market operations. The Balanced Scorecard is viewed as an effective tool to examine the interactions between an organizations and the environment even though challenges are present and must be overcome for successful implementation. In addition, the Balanced Scorecard can also be used to integrate department’s organizations and distribute resources.