In the context of global warming, the Wuhan Urban Agglomeration is actively responding to China’s carbon peak and carbon neutrality goals and striving to achieve a reduction in carbon sources and an increase in carbon sinks. Therefore, it is critical to investigate carbon emissions from land use. This study uses the carbon emission coefficient method to calculate carbon emissions from land use in the Wuhan Urban Agglomeration, analyzes its temporal and spatial changes and differences in urban structure, and couples with the Markov–PLUS model to simulate and predict the carbon emissions of four scenarios of land use in 2035. The research found the following: (1) during the Wuhan “1+8” City Circle stage, carbon sources and emissions increased steadily, with average annual growth rates of 1.92% and 1.99%, respectively. Carbon sinks remained stable and then decreased, with an average annual growth rate of −0.46%. (2) During the Wuhan Metropolitan Area stage—except for 2020 and 2021, which were affected by COVID-19—carbon sources, sinks, and emissions continued to grow in general, and the average annual growth rates increased to 4.46%, 1.58%, and 4.51%, respectively. (3) In terms of urban structure differences, Wuhan is a high-carbon optimization zone; Xianning, Huangshi, and Huanggang are ecological protection zones; other cities, such as Ezhou, Xiaogan, and Xiantao are comprehensive optimization zones; and there is no low-carbon development zone. (4) The multi-scenario simulation results show that carbon sources and emissions are the highest under the economic development scenario, with values of 100.2952 and 9858.83 million tons, respectively, followed by cropland protection, natural development, and low-carbon development scenarios. Under low-carbon development, carbon sinks were the highest, with values of 1.9709 million tons, followed by natural development, economic development, and cropland protection scenarios. The research results are conducive to the formulation of carbon peak and neutrality goals as well as low-carbon development plans for the Wuhan Urban Agglomeration.