Carbon accounting results for the same city can differ due to differences in protocols, methods, and data sources. A critical review of these differences and the connection among them can help to bridge our knowledge between university-based researchers and protocol practitioners in accounting and taking further mitigation actions. The purpose of this study is to provide a review of published research and protocols related to city carbon accounting, paying attention to both their science and practical actions. To begin with, the most cited articles in this field are identified and analyzed by employing a citation network analysis to illustrate the development of city-level carbon accounting from three perspectives. We also reveal the relationship between research methods and accounting protocols. Furthermore, a timeline of relevant organizations, protocols, and projects is provided to demonstrate the applications of city carbon accounting in practice. The citation networks indicate that the field is dominated by pure-geographic production-based and community infrastructure-based accounting; however, emerging models that combine economic system analysis from a consumption-based perspective are leading to new trends in the field. The emissions accounted for by various research methods consist essentially of the scope 1–3, as defined in accounting protocols. The latest accounting protocols include consumption-based accounting, but most cities still limit their accounting and reporting from pure-geographic production-based and community infrastructure-based perspectives. In conclusion, we argue that protocol practitioners require support in conducting carbon accounting, so as to explore the potential in mitigation and adaptation from a number of perspectives. This should also be a priority for future studies.