The ISO 50001 energy management system (EnMS) standard was published in June 2011 and has been widely adopted by organizations from around the world, including Thailand. From 2014–2017, there was a continuous increase in the number of ISO 50001-certified companies in the East Asia and Pacific regions and, more broadly, the world, although this is not consistent with the number of companies that emerged during this period in Thailand. This information shows that the implementation of energy management in some companies may not be sustainable. This research offers a novel method for assessing the quality of energy management in the form of an energy management system sustainability index (EnMS SI) framework, presenting the economic, organizational, energy performance, and environmental aspects of sustainable energy management. Data collection, from a literature review of related research and the EnMS good practices, was implemented in order to select sustainability indicators and further develop a sustainability index for energy management. The analytic hierarchy process (AHP) and weighted arithmetic mean (WAM) were used to establish an EnMS SI. The study results were then assessed and validated using 31 ISO 50001-certified companies in Thailand. Direct interviews and questionnaires were used to obtain responses from energy management representatives. The studied data indicated that an EnMS SI framework can be used in qualitative analyses to effectively determine the sustainability of an EnMS. Significant sustainability indicators, consisting of continuous benefits, top management commitment, and long-term strategic planning, were found. The results also revealed that the EnMS in Thailand has been significantly economically weak. The EnMS SI framework is a tool for assessing energy management sustainability, which allows for the determination of an organization’s actual strengths and weaknesses. The benefits of this framework include the possibility of determining guidelines for correcting and improving the EnMS to achieve sustainability.