Carbon emissions caused by the massive consumption of energy have brought enormous pressure on the Chinese government. Accurately and rapidly characterizing the spatiotemporal characteristics of Chinese city-level carbon emissions is crucial for policy decision making. Based on multi-dimensional data, including nighttime light (NTL) data, land use (LU) data, land surface temperature (LST) data, and added-value secondary industry (AVSI) data, a deep neural network ensemble (DNNE) model was built to analyze the nonlinear relationship between multi-dimensional data and province-level carbon emission statistics (CES) data. The city-level carbon emissions data were estimated, and the spatiotemporal characteristics were analyzed. As compared to the energy statistics released by partial cities, the results showed that the DNNE model based on multi-dimensional data could well estimate city-level carbon emissions data. In addition, according to a linear trend analysis and standard deviational ellipse (SDE) analysis of China from 2001 to 2019, we concluded that the spatiotemporal changes in carbon emissions at the city level were in accordance with the development of China’s economy. Furthermore, the results can provide a useful reference for the scientific formulation, implementation, and evaluation of carbon emissions reduction policies.