Cities worldwide are actively implementing waste classification policies to develop efficient waste management systems that address the growing challenges of waste disposal and promote sustainable development. However, selecting tailored waste classification solutions is challenging due to the intricate interrelationships within the system and the complex trade-offs between different management objectives. This study presents a comprehensive methodology that simulates the entire waste classification management system by integrating the stages of waste generation, source classification, and final disposal, all linked by waste quantities and properties. A multi-objective optimization model is employed to identify optimal technical pathways that balance economic, environmental, and energy objectives. This methodology was applied in Zhangjiagang, a medium-sized city in China, revealing that economically optimal solutions focusing on landfill and composting as disposal pathways could exacerbate environmental impacts, with indicators deteriorating by 23.1 %–419.1 % except for freshwater eutrophication potential. In contrast, a multi-objective optimization solution prioritizing incineration and anaerobic digestion achieves environmental and energy benefits valued at 18.7 USD/t, with a modest increase in economic costs of 5.7 USD/t compared to the base year. The unconstrained optimal scenarios achieve net negative environmental costs and recover 2.0 × 106 MJ of energy. The study recommends moderate and dynamically adjusted kitchen waste separation rates depending on the stage of implementation. Additionally, the findings reveal that the “lock-in” effects of mismatched disposal facilities can significantly escalate costs. In conclusion, this study underscores the importance of systematic design and multi-objective optimization, offering a comprehensive methodology for cities aiming to enhance their waste classification strategies.