In the context of high-quality economic development and coordinated regional development, this paper measures the urban land use efficiency of 275 prefecture-level cities in China from 2003 to 2016, taking into account the unexpected output (environmental pollution), and explores the temporal and spatial evolution of urban land use efficiency through kernel density estimation and spatial autocorrelation analysis. The results show that: (1) From 2003 to 2016, China’s urban land use efficiency showed an overall fluctuating growth, but it remained at a low level. The mean value of urban land use efficiency has been gradually decreasing in east, west and central regions. (2) In the whole country and the eastern, central and western regions, the regional differences have been increasing, and the efficiency values of the whole country and the east have become polarized. (3) Urban land use efficiency shows a weak spatial positive correlation, but the degree of spatial agglomeration is increasing. High-high agglomeration areas are mostly distributed in the southeastern coastal areas, and extend into the central region, while most of the high-low polarized areas are the capital cities of the central and western regions. The low-high depressed areas are scattered around the high-value accumulation areas, some of which have turned into high-high agglomeration areas during the study period, while the low-low homogeneous areas are mainly distributed in the central, western and northeastern regions. Therefore, it is proposed that strengthening the utilization of urban stock land, strengthening the regional cooperation mechanism, and formulating policies which improve the efficiency of land use are effective ways to promote the intensive and economical use of urban land, as well as regional coordinated development.