Rivers play a key role in regulating urban ecology, which can improve urban climate while slowing the heat island effect. As one of embodied energy in the field of ecology, emergy theory can be used to quantitatively evaluate the ecological characteristics of a system. This will help to further explore urban ecological sustainability in this article. In this study, four ecological riverbank reconstruction projects have been executed to restore the ecology along the banks of the Jinchuan River in Nanjing, China, which focus on the key river–lakeside and waterfront space in the main urban area. The LCA–emergy–carbon emission method was applied through a series of indicators, including emergy indexes and carbon emission indicators. It is important to distinguish prior research, and few have utilized this approach on urban waterways and waterscapes. The results illustrate that the reconstruction system has obvious improvement significance to the whole river ecology. This change can also be seen when using LCA–emergy analysis. In a 20-year cycle, the emergy of the material production stage and maintenance phase account for a major emergy share, followed by the construction stage, transportation process, and design process stage. The sustainability (ESI indicator) has been improved after carrying out the reconstruction projects. By choosing water and gravel as the primary material, the carbon emission can be reduced. The water treatment process accounts for the vast majority of carbon emissions. Secondly, gravel also plays an important role in carbon emission. Finally, an improved measure (clean energy reuse) was conducted to enhance the ecology of the reconstruction projects and obtained a significant ecological sustainability boost.