Land eco-efficiency reflects the relationship between economic development and resource utilization, studying the spatio-temporal differentiation of it is conducive to promoting the transformation of land utilization mode to low-carbon intensive direction. In this study, an efficiency index system was built by using resource-capital-labor as the input index, economic-resource-social-ecological benefits as the expected output and carbon emissions as the unexpected output; besides, Super-SBM, Exploratory Spatial Data Analysis, Trend Analysis and Standard Deviation Elliptic Model were conducted to assessed the land eco-efficiency. As results, we found that the average values of land eco-efficiency index were showing a rising trend at first and a falling trend thereafter. Spatially, the difference goes from large to small in the western, eastern, northeast and central China. From the view of spatial differentiation, the high-efficiency areas were concentrated around Chongqing and gradually extended to the northeast. The average efficiency areas mainly distributed in the Pearl River Delta and urban agglomerations around the middle reaches of the Yangtze River. Low-efficiency areas were widely distributed in the central region of China. Furthermore, the spatial autocorrelation coefficient changed from negative to positive and the spatial agglomeration gradually changed to a positive correlation. The main significant correlation types were between High-High areas and Low-Low areas. The significant HH areas formed several groups in the northeast China and Inner Mongolia, and their number increases significantly. The significant LL areas formed a continuous distribution trend in the central and eastern China.