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[Objective] The issue of carbon emission efficiency is of great significance to the realization of the “dual carbon” goal. To reveal the impact of land resource misallocation on carbon emission efficiency, and to explore its path, it provides a scientific basis for promoting regional green and low-carbon development from the perspective of land resource allocation. [Methods] Based on the theory that land resource misallocation affects carbon emission efficiency, and using the spatial Durbin model and mediation effect model, this study examined the spatial effect of land resource misallocation on carbon emission efficiency and mechanism of 108 cities in the Yangtze River Economic Belt from 2004 to 2020. [Results] (1) The indirect effect of land resource misallocation on carbon emission efficiency is far greater than the direct effect, and the preferential allocation of land will do more harm by the negative externalities of neighboring cities. (2) For different locations and cities of different sizes, land resource misallocations and their spatial effects vary greatly. (3) Land resource misallocation has a complex mechanism for affecting carbon emission efficiency, which can reduce regional carbon emission efficiency through inhibiting innovation ability development, slowing industrial structure upgrading, and blocking new-type urbanization. [Conclusion] In order to improve regional carbon emission efficiency, the Chinese government should accelerate the market-oriented reform of land factor allocation, strengthen the concept of regional cooperation and win-win cooperation and collaborative governance capacity. Based on these results, we argued that increasing the support for technological innovation, optimizing the industrial structure, and actively and orderly promoting new-type urbanization are the effective ways to increase carbon emission efficiency in the future.