[Objective] The measurement of land space use efficiency and comprehensive spatial zoning in Yunnan Province were studied, considering carbon neutrality, provide a reference for proposing differentiated low-carbon and high-efficiency land space development strategies. [Methods] Using 2020 panel data of 16 municipal units in Yunnan Province, the spatial utilization efficiency of the national territory under the low-carbon perspective were measured based on the non-expected output super-efficiency SBM model, and comprehensive zoning were performed considering the carbon efficiency index; subsequently, optimization suggestions for each zone are put forward. [Results] ① The carbon emission in Yunnan Province in 2020 was 1.23×10⁸ tonnes, with production-space-related emissions accounting for a much larger proportion than living-space-related emissions: the former was almost 31 times as much as the latter. Further, carbon absorption was 1.40×10⁷ tonnes, which is only one-tenth of the carbon emission. ② In 2020, the land space utilization efficiency of Yunnan Province was only 0.628, showing a spatial distribution pattern that is higher in central and northwestern Yunnan, and lower in eastern and southwestern Yunnan. Specifically, only Xishuangbanna, Diqing and Yuxi reached high efficiency utilization, with the maximum efficiency of 1.43, while Zhaotong had the lowest utilization efficiency of 0.49. ③ Based on the land space utilization efficiency and the carbon efficiency index, 7 comprehensive zones-Low carbon retention-High efficiency, Carbon sink function-High efficiency, Carbon sink function-Moderate efficiency, Carbon sink function-Low efficiency, Carbon intensity control-High efficiency, Carbon intensity control-Moderate efficiency, and High carbon optimization-Low efficiency-are derived, and a differentiated governance strategy for each zone is put forward. [Conclusion] At present, carbon absorption in Yunnan Province is far from enough to offset carbon emissions, and the overall performance is carbon source. The utilization of territorial space is still relatively extensive, and there is great potential to improve utilization efficiency. The distribution of territorial space utilization efficiency has obvious regional imbalance, and attention should be paid to the formulation of low-carbon development and efficient utilization strategies for territorial space.