[Objective] Reducing carbon emissions is important for Yunnan Province to actively serve and integrate into the national development strategy as it strives to become a vanguard in the construction of ecological civilization. {Methods] The spatio-temporal change and spatial correlation of eco-environmental quality in Yunnan Province were determined based on risk-screening environmental indicators (RSEI), and the priority of ecological restoration in Yunnan Province was identified by combining these results with regional ecosystem carbon reserves and an ecological protection red line in order to provide a scientific basis for low-carbon sustainable development of Yunnan Province. [Results] (1) The average value of RSEI in Yunnan Province showed an "S-shaped" trend over the past 22 years, with 2005 and 2011 being the inflection points of increasing and decreasing RSEI, respectively. (2) From 2000 to 2022, the spatial eco-environmental quality was characterized as "high in the west and low in the east". The ecological environmental quality in the western region was good, while the ecological environmental quality in the central urban agglomeration and the eastern karst region was poor. (3) From 2000 to 2005, the ecological environmental quality became better under the influence of the policy of returning farmland to forests. From 2005 to 2011, the ecological environmental quality decreased significantly due to drought and the drastic expansion of construction land. 2000–2016 was a period of recovery after drought. Except for the areas with rapid urbanization in central China, the ecological environmental quality in other areas gradually recovered. Due to the influence of national policies in 2016, the ecological environmental quality further improved. (4) The ecological environmental quality of Yunnan Province showed obvious spatial global and local autocorrelation; (5) The carbon reserves of Yunnan Province initially increased and then decreased from 2000 to 2022, and the total carbon reserves decreased by 2.38×107 t in 22 years. Carbon reserves showed a zonal distribution characterized as "high in the north and south, and low in the central region". (6) The high priority areas for ecological restoration in Yunnan Province were mainly located in the north and east, accounting for about 18.08% of the total area, while the medium priority areas for ecological restoration were more widely distributed, accounting for about 70.17% of the total area. The general priority areas for ecological restoration were mainly located in Pu′er City and other places, accounting for about 11.76% of the total area. [Conclusion] The ecological environmental quality of Yunnan Province exhibited distinct patterns in time and space from 2000 to 2022. Based on these results, the ecological restoration area should be divided, and the ecological environment should be controlled according to local conditions in order to promote ecological and sustainable low-carbon development in Yunnan Province.