Carbon capture and storage (CCS) is a critical technology used for mitigating climate change by capturing carbon dioxide emissions from industrial sources and storing them underground to prevent their release into the atmosphere. Despite its potential, optimizing CCS systems for cost-effectiveness and efficiency improvement remains a significant challenge. In this paper, the optimization of CCS systems through the development and application of two mathematical optimization techniques is introduced. The first technique is based on using a superstructure optimization model, while the second technique relies on applying a goal programming optimization model. These models were solved using LINGO software version API 14.0.5099.166 to enhance the efficiency and cost-effectiveness of CCS systems. The first model, seeking to maximize the exchange of CO2 flowrate from sources to sinks, achieved a CO2 capture rate of 93.36% with an annual total cost of USD 1.175 billion. The second model introduced a novel mixed-integer non-linear programming (MINLP) approach for multi-objective optimization, targeting the minimization of total system cost, alternative storage, and unutilized storage while maximizing CO2 load exchange. The application of the second model, when prioritized to maximize CO2 flowrate exchange using the goal programming technique, resulted in a cost reduction of 36.46% and a CO2 capture rate of 75.87%. In contrast, when the second model prioritized minimizing the total annual cost, a 48% cost reduction was achieved, and the CO2 capture rate was decreased by 68.37%. A comparison of the two models’ results is presented. The results showed that the second model, with the priority of maximizing CO2 capture, provides the best economic–environmental objective balance, which offers notable cost reductions while keeping an efficient CO2 capture rate. This study highlights the potential of advanced mathematical modeling in increasing the feasibility of CCS as one of the very important strategies of mitigating climate change and reducing global warming.