In view of the carbon-hydrogen-oxygen symbiosis networks (CHOSYNs) in eco-industrial parks (EIPs), a multi-objective optimization and decision-making method is proposed based on multi-scale atomic targeting method, considering economic and environmental factors and the reuse of by-product of carbon-hydrogen-oxygen compounds, and the optimal scheme is obtained from the alternatives. In this method, the mathematical programming method is adopted, and the global optimization is carried out with the minimum total annual cost (TAC) and carbon-dioxide annual emission (CAE) as the objective functions respectively, and the mixed-integer nonlinear programming (MINLP) model is established. Using the ε-constraint method, the CAE is transformed into constraint conditions, and the Pareto front of the TAC and CAE is obtained. It is found that the TAC is inversely proportional to CAE. The linear programming technique for multidimensional analysis of preference (LINMAP) and technique for order preference by similarity to ideal situation (TOPSIS) methods are used to make the optimal decision on the Pareto frontier. It is found that they choose the same point as the optimal decision. Based on the proposed method, an industrial park is optimized. The results show that the rational use of the existing by-product of carbon-hydrogen-oxygen compounds can reduce the cost of the raw materials, and reduce the TAC and CAE by 63.44% and 76.99%, respectively.