Environmental pollution, as a byproduct of economic growth, causes negative pressure on human health. Its sustainability management performance is closely bound up with the ecological carrying capacity. Due to the limited carrying capacity of ecosystems to pollutants, the hidden costs of pollutants may increase when pollutants flow and spread. This is an external manifestation of the internal resource imbalance within the ecosystem, restricting the sustainability of economy and environment and overlooked by most studies that target sustainability performance evaluation. Thus, this study considers the internal resource imbalance during the sustainability performance evaluation for the first time in the context of the interaction among economy, environment, and human health, by constructing a production-treatment-health framework, proposing an internal resource imbalance index and developing an additive aggregation network data envelopment analysis model with the semidefinite programming technology. This study takes 30 Chinese provinces from 2012 to 2017 as the research objects and confirms the effectiveness of sustainability management in terms of water pollution purification and water ecological construction.