It has been more than forty years since the ecological network analysis was proposed, and its theories and applications have developed rapidly. Until 2002, the method had only been used to study urban ecosystems and to analyze interconnected networks, including multiple actors and ecological flows. Presently, the application of ecological network analysis to urban ecosystems includes its use at multi-scales and based on different indicators. It has been subdivided into Network Environ Analysis and Ascendency Analysis; and the multi-scales indicate regions comprised by cities and cities including industrial sectors. However, there are still aspects of the method that need to be improved, such as the application of multi-scales (e.g., using cities as nodes in a network or specifying sectors in urban systems) or the combined analysis of different indicators, and these limitations restrict the use of the method for urban planning and design. To continue the development of ecological network analysis in urban ecosystems, three main perspectives should be addressed:(1) the application of ecological network analysis at multi-scales, such as urban agglomerations and systems and industrial parks and communities, and the development of nested ecological networks; (2) the combination of Ascendency and Network Environ Analyses to develop an assessment system or method from external and internal attributes; and (3) emphasis on the importance of natural actors in urban ecosystems, along with merging socio-economic and natural actors to establish ecological networks with different precision.