Aquaculture is the fastest growing food production industry in terms of annual growth rate and has become an important contributor in supplying essential macro-and micro-nutrients for the global population. However, there is a great deal of uncertainty in its further development due to the high and increasing pressure of environmental challenges and of resource constraints. To achieve overall sustainable development of the aquaculture sector in China, the dominant producer of farmed seafood in the world, the priority is to clarify the sustainability of major aquaculture production systems (APSs) and to seek a holistic approach to improve their sustainability. Here the sustainability of ten major types of APSs in China, was evaluated comparatively by three objective and subjective methods involving eleven social, economic, environmental, and resource criteria. Accordingly, ecological intensification of aquaculture systems (ELIAS), integrating anthropogenic inputs with aquaculture ecosystem services, is proposed to improve the sustainability of these APSs. ELIAS that should be widely adopted by the multiple stakeholders provides a feasible solution to realize the goals of increasing aquaculture outputs with less negative environmental influence while saving energy at the same time.