Rapid urbanization exacerbates urban metabolic activities associated with irreversible environmental degradation. Evaluating urban metabolic performance is an effective method to meet targets for sustainable development in contemporary urban areas. Neighborhoods, which are regarded as the basic parts of cities, can detail the metabolic structure and interactions from a bottom-up perspective. In consequence, this study proposed an eco-efficiency model which combined emergy synthesis and slack-based measure data envelopment analysis. A case study with questionnaire and statistical data for eight communities in Chongqing, China was used to shed a light on the properties of emergy metabolic flows and eco-efficiency. The results showed that the study communities heavily depended on external resources. Intense communal activities within relatively small geographic areas caused immediate surroundings to suffer from enhanced environmental pressures. Eco-efficiency performances were mostly invalid, and a significant heterogeneity existed among communities. Enhancing the performance of renewable and non-renewable resources whilst also reducing the production of wastes was essential to improve the overall eco-efficiency of local communities. To assist with this, a neighbor-level sustainable renewal framework was proposed which took account of metabolic flows and communal renewal operations. The findings of this study can provide a paradigmatic example for urban renewal projects elsewhere that embed metabolic performance in neighborhood redevelopment.