The need to create sustainable cities has led to increasing concern on achieving healthy spatial metabolic interactions and system sustainability. Based on emergy synthesis and an urban spatial conceptual framework, we employ a set of seven emergy-based indicators to evaluate the sustainability of spatiotemporal metabolism for Xiamen, southeast China, using 1987–2007 land use and socio-economic statistic data. The results show a general improvement in socio-economic performance (emergy intensity, GDP emergy ratio, and emergy turnover ratio), but a steady deterioration in environmental performance (emergy self-support ratio, emergy density, and waste density) during the period 1987–2007. An increasing environmental and socio-economic metabolic gap exists between the built-up urban sprawl region (USR) and urban footprint regions (UFRs) due to resource privation and environmental space occupation, potentially undermining system sustainability. Compared to other Chinese cities and provinces, Xiamen still exhibited relatively weaker sustainability in 2002 due to increasing pressure on ecosystem health. Environment-oriented, society-oriented and cross-boundary-oriented metabolic strategies should be incorporated into future city development to foster urban system sustainability.