Sustainable development of cities requests to achieve the synergistic goals of water security and climate change, that is, enhancing water security and reducing carbon emissions simultaneously. Motivated by this, in this paper, a developed slacks-based measure model in data envelopment analysis, which treats carbon emissions as an undesirable output, was carried out to explore the efficiency of urban water supply under carbon emission constraints. Taking China as a case study, the main findings suggested that (i) China's urban water supply produced huge carbon emissions, which is approximately equal to the total carbon emissions of Kyrgyzstan; (ii) the carbon emission intensity of urban water supply has increased by about 177% compared with seven years ago; (iii) the average urban water supply efficiency is significantly lower than that without carbon emission constraints; and (iv) the more abundant water resources the city has, the worse the urban water supply efficiency is. Based on these observations, major factors influencing the efficiency of urban water supply under carbon emission constraints were identified by using ordered probit and Tobit models. Finally, feasible paths to achieve the synergistic goals were provided in terms of society, economy, and the environment.