On the basis of DMSP/OLS and NPP-VIIRS night light images, this study realized carbon emission estimations based on the municipal level from 1999 to 2017, compensating for the characteristics of incomplete statistical data and different statistical calibers. On this basis, the epsilon-based measure (EBM) super-efficiency model and the global Malmquist-Luenberger (GML) index are used to measure the urban land use efficiency (ULUE) and urban land total factor productivity (ULTFP) of the three urban agglomerations under the carbon emission constraints from 1999 to 2017. The following conclusions are drawn through research. (1) The correlation coefficient between the total value of night light pixels and energy consumption carbon emissions was relatively high in the three major urban agglomerations during 1999-2017, and they all passed the significance test of 1%. (2) The ULUE of the three major urban agglomerations generally shows a downward trend and then an upward trend, and spatial heterogeneity is obvious. The spatial distribution of the average level of ULUE is Pearl River Delta Urban Agglomeration (PRDUA) > Yangtze River Delta Urban agglomeration (YRDUA) > Beijing-Tianjin-Hebei Urban agglomeration (BTHUA). (3) The ULTFP of the three major urban agglomerations are all showing an increasing trend, but the geometric mean of URTFP in the PRDUA, BTHUA, and YRDUA decreases successively. Technological progress is the main driving force to promote the progress of ULTFP in each urban agglomeration. (4) The kernel density estimation shows a significant gap in ULUE between the three major urban agglomerations in China, and a phenomenon of polarization or multipolarization is observed. The main reason is the hysteresis of technology diffusion.