The comparative advantage of land use efficiency can provide effective support for upgrading the industrial structure and optimizing the allocation of land resources. According to the agricultural industry and non-agricultural industry, the evaluation index system of land use efficiency is constructed by difference. By using China’s provincial panel data in 2010, 2015 and 2019 as an empirical test and comprehensively employing the comparative advantage model, GIS spatial analysis model, geographical weighted regression model and other algorithms, the land use efficiency and the comparative advantage were measured and evaluated to explore the evolution of spatial and temporal patterns and identify the influencing factors. The results showed the following: (1) The overall efficiency of agricultural land grew steadily, with regional differences transforming from expanding to narrowing, forming a gradually decreasing overall trend from the southeast coast to the northwest inland, and from the eastern plain to the western plateau. The overall efficiency of non-agricultural land was generally low, presenting an overall growth trend, and regional differences were progressively expanding, still showing a gradually decreasing trend in the eastern, central and western regions. (2) The overall comparative advantage of agricultural land efficiency showed a gradual decline trend, and the differences between regions were further narrowed. The high-value regions were still concentrated in the regions with superior agricultural resource endowment and showed a dominant advantage of the agricultural industry. The overall comparative advantage of non-agricultural land efficiency showed an increasing trend. The high-value areas were concentrated in urban agglomeration, metropolitan areas and other areas with high non-agricultural land efficiency, as well as the vast remote areas such as the northwest and southwest where the agricultural land efficiency was extremely low and the comparative advantage of non-agricultural land efficiency improved. (3) The spatial concentration of the comparative advantage of agricultural land and non-agricultural land efficiency was not obvious, which indicates that the comparative advantage of industrial land in China has not yet formed a trend of agglomeration development, but there were dense and obvious high-high agglomeration areas or low–low agglomeration areas in some local regions. (4) Significant regional differences were found to exist in the impact of various factors on the comparative advantages of agricultural land efficiency and non-agricultural land efficiency. The comparative advantage of land use efficiency can be relied on to promote the optimization and adjustment of industrial structure and guide the efficient allocation of land resources.