Comprehensive evaluation of the sustainability of paddy ecosystems is key to success in paddy ecosystem management. In this research, we propose a novel quantitative method for sustainability evaluation based on the net value of ecosystem services, which consists of a new elasticity-based sustainability evaluation framework for agricultural ecosystems. The sustainability of ecosystems, evaluated through ecosystem elasticity, is reflected in seven measurable indicators within three domains: ecological, which includes the proportion of paddy area, per capita cultivated land area, and annual waste water discharge per capita; economic, which includes the agricultural economy level and urbanization rate; and social, which includes education of farmers and rural medical level. The evaluation approach we propose constitutes an important contribution to sustainability evaluation methodology. We apply the proposed approach to evaluate the sustainability of China’s paddy ecosystems. The results suggest that the overall paddy ecosystem elasticity in China was on the rise in 2009–2017, indicating the weakening of anti-interference ability and stability of the paddy ecosystem and the deterioration of paddy ecosystem sustainability. Our results also reveal obvious sustainability imbalance in paddy ecosystems across different regions of China. These findings offer empirical evidence substantiating the urgent need for Chinese governmental initiatives to improve the sustainability of paddy ecosystems, particularly those in the Northeastern region. The findings also necessitate inter-regional collaborations, especially collaborations between adjacent paddy ecosystems, to institute cross-regional standards and policies pertaining to the sustainability of paddy ecosystems. The results from the evaluations of China’s paddy ecosystems may serve as a wake-up call for other countries to assess the sustainability of their own ecosystems using the approach we propose. The findings are also likely to raise the awareness of ecosystem sustainability and its evaluation, and promote global ecosystem sustainability research.