The stability and efficiency of the waste supply chain (WSC) is related to the urban environment. This study constructed a framework of barriers to coordinating the WSC based on four perspectives: the costs and benefits, mechanisms involved, behaviors of the subjects, and technologies and standards used. We used an analytic network process based on the fuzzy decision-making trial and evaluation laboratory to calculate the centrality and weight of each barrier factor, and we determined the critical barriers to coordination by combining their results. A causality diagram of the barriers was drawn, and a scheme of coordination of the WSC was designed based on a closed-loop supply chain around the critical barriers. The results show that contradictions in benefits between subjects, contradictions between economic and social benefits, excessive subsidies, the failure of the market mechanism, the lack of a mechanism for supervision, and blocked information and distrust among the subjects are the five most critical barriers to the coordination of the WSC, with excessive subsidies the root cause of the lack of coordination. The subsidy for direct waste disposal should be used to reduce the cost of the operation of the WSC, waste recycling should be improved, an information-sharing platform should be built, and the cost of recyclable waste for manufacturers should be reduced to improve the efficiency of the WSC.