It is of great theoretical and practical significance to understand and explore the regional land use carbon budget and to construct a carbon ecological compensation model, which can guide the regional low-carbon coordinated development and promote the achievement of carbon neutrality. This paper investigates the principle of carbon ecological compensation based on land use carbon budget, and takes Wuhan Urban Agglomeration as the empirical research object. Based on the difference in regional land use carbon budget, the carbon ecological compensation standard of each county (city, district) in urban agglomeration is estimated under the carbon neutrality goal, and the order of carbon ecological compensation payment or compensation is clarified. The results showed that:(1) during the study period, there were significantly spatial differences in net carbon emission from land use among counties (cities, districts) in the urban area. The net carbon emission from land use showed the spatial distribution characteristics of high in the central and western parts of the urban agglomeration and low in the northern, southern, and eastern parts, and the spatial distribution characteristic was gradually strengthened. (2) There were 14 carbon ecological compensation payment zones in the Wuhan Urban Agglomeration, mostly located in the central and western parts of the urban agglomeration, including 5 priority payment zones, 6 secondary payment zones and 3 potential payment zones. (3) There were 25 carbon ecological compensation reception zones in Wuhan Urban Agglomeration, mostly located in the eastern part of the urban agglomeration and peripheral areas, including 5 priority reception zones, 9 secondary reception zones, and 11 potential reception zones, and differential countermeasures for low carbon development were proposed for different types of zones. And it also proposed the differentiated low-carbon development countermeasures for different types of payment and reception zones.