This study analyzes cities in China at the prefecture level and above to calculate indices for "urban economic efficiency" (the relationship between input factors and output) and "urbanization economic efficiency" (the relationship between newly increased output and increased economic input), based on the Stochastic Frontier Analysis (SFA) method. We compare and analyze the factors influencing change and their spatial distributions. The results show that capital and labor rather than urban land could effectively improve urban and urbanization economic efficiency. And, although the proportion of wages to GDP has a significant negative impact on urban economic efficiency, for social equity and stability, the proportion should be increased; if appropriate, it would not significantly reduce urbanization economic efficiency. Additionally, population density, population urbanization rate, and government fiscal expenditure significantly positively impact urban and urbanization economic efficiency. However, we also found that increases in the degree of industrial structure deviation and urban landscape fragmentation are harmful to urbanization economic efficiency. In terms of spatial distribution, the urbanization economic efficiency of most of China's northeastern and eastern coastal areas is significantly lower than that of other regions; at the same time, the urban economic efficiency of most of these cities has been decreasing, especially in the northeast, which warrants greater policy attention.