Since the 1970s, governments around the world have developed environmental regulations and environmental management system (EMSs). Public and private enterprises are obligated to comply with EMSs to prevent environmental pollution. After the International Organization of Standardization (ISO) published the ISO 14001 EMS in September 1996, environmental certification became a focus of attention for enterprises worldwide. Subsequently, various EMSs, such as the ISO 14064-1 Greenhouse Gas Emission Auditing System in 2006 and the ISO 50001 Energy Management System in 2011, have been developed. Governments can demand environmental certification to enforce compliance with environmental regulations. Furthermore, environmental certification can motivate enterprises to improve environmentally relevant practices, conserve energy, and lower costs. This study establishes an ontological knowledge model of shareable and reusable environmental certification index systems. According to this knowledge model, an environmental certification system, an environmental performance index system, and a leather-industry-exclusive environmental certification system were created using the Web Ontology Language (OWL) found in the Protégé platform. The relationship between the EMSs and the performance indices was then generalized to explain the certification systems and their attainable performance indices to enterprise owners. Thus, enterprise owners can select applicable EMSs according to this EMS ontology.