As the impact of emerging pollutants (EPs) on human health and ecosystems becomes significant, attention is being drawn to the treatment of EPs. Unlike conventional pollutants (e.g., chemical oxygen demand, biochemical oxygen demand, SO2, NO x , etc.), EPs have relatively short history of use and production, or have their hazards be identified only recently, and thus are largely beyond the scope of current laws or regulations on environmental pollutants. Synthetic chemicals and unintentionally released chemical substances constitute an important source of EPs. EPs have diverse chemical structures and can take varied forms, including molecules, polymers, and aggregates. EPs can be released into the environment via multiple routes during the life cycle of products that contain corresponding chemicals. In the environment, EPs can be persistent or pseudo-persistent due to continuous release and resistance to degradation. EPs can exert a variety of hazardous effects, including endocrine disruption, carcinogenicity, mutagenicity, etc. In addition, the chronical effects tend to be insidious. All these features have complicated the treatment and control of EPs, resulting in high cost for restoring the contaminated environment. Hence, it is recognized that the key to the treatment of EPs is to prevent potential pollution of the corresponding chemicals. In order to address the issues of EPs, environmental systems engineering (ESE) thinking is required. Environmental issues such as ecological damage and environmental pollution can be regarded as human activity-induced devastation to the structure and function of the Earth surface system, which involves two EPs or chemicals-related processes: (1) The sources, flows and sinks of EPs or chemicals in the human society and natural environmental system, which are informative for controlling policies and strategies to intervene; (2) the effects of EPs or chemicals on the human society system, ecosystem and inorganic environmental system, which provide the basis for setting “objective functions and constraint conditions” for sustainable development of the system. Briefly, ESE for the treatment of EPs and the risk management of chemicals, aims to realize the simulation of systems evolution under various treatment scenarios, by modeling and analyzing the above EPs and chemicals-involved processes in the human society and the natural environmental system. With the constraints on the sustainability of human society, the objective functions, i.e., the economic and social benefits of chemicals and related products, are maximized. Then, the best strategies and practice for the treatment of EPs could be reasonably selected. Several ESE technologies are discussed, among which material flow analysis and life cycle assessment could track the sources, flows, and sinks of chemicals in the human society-economy system, and further quantify their impacts on the environment. Computational toxicology could, via in silico simulations, predict the distribution and fate of EPs, estimate the exposure of human and ecological species to the EPs, and evaluate the adverse effects of EPs on human and ecological species under certain exposure levels. Green chemistry, namely “benign by design”, on the other hand, aims to diminish the use of hazardous feedstocks and the release of waste, and eventually design and produce chemicals with low or zero hazards. All these ESE technologies combined with the relatively conventional process control and terminal treatment technologies, are promising for supporting the risk prevention and control of chemicals, as well as the effective treatment of EPs.