Exploring how land resource allocation approaches that once drove China’s rapid economic growth affect carbon emissions (CE) is important for achieving green and low-carbon sustainable development of Chinese cities. This paper systematically has sorted out the mechanism of the impact of land resource misallocation (LRM) on CE. Then, the impact of LRM on CE is empirically tested in multiple dimensions based on data from 216 cities in China from 2011-2019. The results show that: (1) In terms of impact effects, LRM significantly exacerbates CE and passes the robustness test. The comparison of time-series differences reveals that the impact of LRM on CE decreases significantly as the reform of market-based allocation of land factors deepens. (2) In terms of impact mechanisms, LRM significantly exacerbates regional CE through mechanisms such as influencing industrial structure, inhibiting technological innovation, and weakening industrial agglomeration. (3) In terms of threshold effects, economic development levels and fiscal decentralization significantly affect the impact of LRM on CE. This study offers a scientific foundation for advancing regional green and low-carbon development through the lens of land resource allocation.