Emergy analysis, which both considers the economic aspect and the natural contribution through meaningful comparison across different systems, has been proved to be a powerful tool to assess the ecological economic systems and processes, especially in the mariculture field. In this paper, emergy analysis method is used for establishing a related index system to analyze the large yellow croaker system in Dongji. System indices such as TR, EPD, ELR, EYR, PEEI, EER_Y, ESI and EISD were applied to characterize the resource use, environmental impact and the overall sustainability of the studied system. And the data obtained through the comparison of large yellow croaker aquaculture system in Dongji island and three aquaculture systems surrounding the Pearl River Estuary was discussed. The results showed that the TR of large yellow croaker aquaculture system is 1.46×10⁶sej/J, which was in the middle of three aquaculture systems surrounding the Pearl River Estuary, but lower than the average value of systems studied before. The EPD of large yellow croaker aquaculture system is 2.07×10¹⁷sej·hm^-2·a^-1, and ELR is 91.10. And in this study, purchased external resource emergy inputs achieved a greater effect than putting renewable environmental resource emergy in large yellow croaker aquaculture system. And results showed the system had more dependence on purchasing external resource emergy inputs. The ESI is 0.011, EISD is 0.02, which indicate that the large yellow croaker aquaculture system is less sustainable. Based on sensitivity analysis, ESI and EISD these two sustainable indicators are elevated, due to half reduced the inputs amount of fingerlings and double increased the inputs of rain chemical. Based on above analysis, getting two effective solutions: (1) By reducing feed inputs, improving the feed utilization efficiency, aquaculture facilities deployed in areas with more rainfall, to improve local renewable resources inputs proportion; (2) By improving the labor efficiency or breeding technology from depending relying on labor to relying on technology, to reduce the purchased external resources inputs.