The characteristic “high input and output” in protected production has caused some environmental and ecological issues. Hence, emergy-based sustainability assessments are necessary and valuable. However, traditional emergy analysis is time consuming, tedious, and inefficient. Such disadvantages can be addressed by the integration of emergy analysis with information technology. This paper reports the development of the emergy-based sustainability decision assessment system (ESDAS) for protected grape cultivation systems. This system was established by first analyzing the business process, users, and requirements through survey, and the findings of which were used to design the system’s function, architecture, database, model base, and knowledge base with a combination of emergy methods. The results showed that ESDAS passed the system test and achieved the real-time calculation of emergy data and the automatization of emergy analysis. Therefore, this research is a beneficial attempt to apply information technology in improving the efficiency of sustainability assessments. The results also revealed that the protected grape cultivation system is characterized by a heavy dependence on purchased and non-renewable resource emergy, lower emergy yield ratio, higher emergy investment rate and environmental loading ratio, and lower emergy sustainability index. Some suggestions were made to improve the sustainability of the protected grape system.