Ensuring equitable allocation of carbon emission responsibilities at the city level is crucial for effectively mitigating climate change. However, traditional allocation methods like production-based accounting (PBA) and consumption-based accounting (CBA) encounter double-counting problems at this scale. This study for the first time addressed the ignored externality of carbon emissions among bilateral trading partners at city scale, achieving equitable carbon emission responsibility reallocations using the economic welfare gain-based (EWG) method. Examining 313 cities in China using a multi-regional input-output model, the highest carbon emission responsibilities are identified in Baotou at 400.7 Mt., followed by Yunnan (189.9 Mt) and Dalian (166.7 Mt). In this case, the EWG method reallocates producer and consumer responsibilities in bilateral trades. Among the 313 cities, emission responsibilities from 198 are situated between PBA and CBA, avoiding one-sided assignment of emissions based solely on either principle. A comparative analysis of allocation methods in China further indicates a predominance of production responsibility, mirroring a similar trend between EWG and PBA; a significant portion of producer responsibilities are identified within EWG. The results of this work may offer a fairer and economically sound basis for allocating emission responsibilities among cities, thereby facilitating more effective emission reduction strategies.