Carbon ecological efficiency reflects the relationship between carbon emission and socio-economic outputs and is an important characterization for regional sustainable development. We considered the Pan-Yangtze River Delta (PYRD)-one of the most economically developed and fast-changing regions in China-as a case area, and analyzed the spatial pattern of carbon ecological efficiency at city levels based on two indicators, economic output and population carrying efficiency, which indicated the economic and social outputs of carbon emission respectively. Spatial correlation and multiple regression analyses were adopted to analyze the influencing factors of carbon ecological efficiency. The main results and conclusions were as follows:the economic output and population carrying efficiencies, which showed different changing trends, increased by 97% and decreased by 68% from 2000 to 2014, respectively. The economic output efficiency, which increased from 0.23 to 0.34, exhibited a higher spatial agglomeration degree than that of the population carrying efficiency, which was lower and remained basically stable in 2000 and 2014. Cities at the peripheral region had higher economic output efficiency than those at the core region did in 2000, but the situation was reversed in 2014. The population carrying efficiency of cities at the peripheral region were always lower than that of cities at the core region. Some cities at the core region or along the Yangtze river with higher developmental levels than others, such as Shanghai and Nanjing, showed higher economic output efficiency and their decrease in population carrying efficiency was slower than that of most cities in PYRD, which indicated that their comprehensive carbon ecological efficiency were higher than other cities. The results of the influencing factors analysis indicated that the economic output and population carrying efficiencies were affected by similar factors, but their influence on the two indicators differed in intensities and directions. The major influencing factors of the economic output efficiency were specific to the economic structure, especially the proportion of service industry accounting for the gross domestic product (GDP). However, the influencing factors of the population carrying efficiency were more complicated, and included GDP per capita, urbanization rate, and the proportion of R&D input accounting for the GDP. This research revealed that the trends of carbon ecological efficiency could vary considerably with different measuring indicators, and PYRD was a case with increasing economic output efficiency and decreasing population carrying efficiency. Moreover, the major influencing factors of the various measuring indicators also differed and, therefore, it was difficult to promote the economic and social benefits with similar regulatory measures. Some of the more developed cities exhibited higher economic output efficiency and slower decreasing population carrying efficiency than the less developed cities did, and their measurement could be used to promote both economic and social benefits simultaneously. We concluded that the main orientation of policymaking was to promote population agglomeration, optimize the industrial and energy consumption structure, and increase energy utilization efficiency.