In order to develop a sound material-cycle society, cost-effective municipal solid waste (MSW) management systems are required for the municipalities in the context of the integrated accounting system for MSW management. Firstly, this paper attempts to establish an integrated cost–benefit analysis (CBA) framework for evaluating the effectiveness of MSW management systems. In this paper, detailed cost/benefit items due to waste problems are particularly clarified. The stakeholders of MSW management systems, including the decision-makers of the municipalities and the citizens, are expected to reconsider the waste problems in depth and thus take wise actions with the aid of the proposed CBA framework. Secondly, focusing on the financial cost, this study develops a generalized methodology to evaluate the financial cost-effectiveness of MSW management systems, simultaneously considering the treatment technological levels and policy effects. The impacts of the influencing factors on the annual total and average financial MSW operation and maintenance (O&M) costs are analyzed in the Taiwanese case study with a demonstrative short-term future projection of the financial costs under scenario analysis. The established methodology would contribute to the evaluation of the current policy measures and to the modification of the policy design for the municipalities.