Establishing industrial ecosystems (IEs) is a viable approach for the sustainable development of industries. The ultimate objective of an IE is to minimize the material and energy consumption and reduce or even eliminate waste disposal through various recycle and reuse mechanisms. Yet, a rigorous scientific approach for the analysis and design of sustainable IE is lacking. The major obstacles include the challenge of evaluating each dimension of the "triple bottom line" of sustainability, handling the complex interdependency among different members, and the need of a holistic decision-making/decision-analysis method across different scales, from the individual production unit up to the ecosystem. To tackle this difficulty, the improvement of economic and environmental sustainability of IEs is defined as a multilayer multi-objective optimization problem in this paper. A novel Hierarchical Pareto Optimization Methodology is introduced to achieve the most sustainable solution. This methodology provides a systematic and flexible framework to solve multiscale, multidimensional problems, and it provides clear guidance for improving sustainability. The effectiveness of this approach is demonstrated by a case study.