Eco-efficiency, as one of the evaluation tools for sustainable development performance, has been a widely discussed topic in academia for the past several decades. However, the existing research on eco-efficiency is rather homogeneous. Most of it is based on the construction of a system of indicators that includes ecological constraints to evaluate its overall eco-efficiency, but it treats the eco-economic system as a ‘black box’, ignoring the fact that it is actually composed of several sub-systems. In this paper, based on a two-stage resource-environment system perspective, we construct a Super-NEBM model considering undesirable outputs to measure urban ecological efficiency; a spatial Durbin model is then used to analyse its influencing factors. The results indicate that (1) China’s urban eco-efficiency levels are fluctuating, with a decreasing “east-central/northeast-west” trend. (2) The spatial heterogeneity of ecological efficiency levels in Chinese cities is obvious, with significant spatial agglomeration effects. (3) There are positive spatial spillover effects on the ecological efficiency of Chinese cities; economic development, industrial structure, financial development, population density, innovation capacity, infrastructure, marketisation and informatisation all have important direct effects on urban ecological efficiency; in addition, economic development, financial development, population density, marketisation, informatisation and foreign investment all have significant indirect effects of varying degrees.