To completely understand the effects of urban ecosystems, the effects of ecosystem disservices should be considered along with the ecosystem services and require more research attention. In this study, we tried to better understand its formation through the use of cascade flowchart and classification systems and compare their effects with ecosystem services. It is vitally important to differentiate final and intermediate ecosystem disservices for understanding the negative effects of the ecosystem on human well-being. The proposed functional classification of EDS (i.e. provisioning, regulating and cultural EDS) should also help better bridging EDS and ES studies. In addition, we used Beijing as a case study area to value the EDS caused by urban ecosystems and compare the findings with ES values. The results suggested that although EDS caused great financial loss the potential economic gain from ecosystem services still significantly outweigh the loss. Our study only sheds light on valuating the net effects of urban ecosystems. In the future, we believe that EDS valuation should be at least equally considered in ecosystem valuation studies to create more comprehensive and sustainable development policies, land use proposals and management plans.